API Documentation¶
This is the API documentation for msprime
, and provides detailed information
on the Python programming interface. See the Tutorial for an
introduction to using this API to run simulations and analyse the results.
Simulation model¶
The simulation model in msprime
closely follows the classical ms
program. Unlike ms
, however, time is measured in generations rather than
in units of \(4 N_e\) generations, i.e., “coalescent units”.
This means that when simulating a population with diploid effective size \(N_e\),
the mean time to coalescence between two samples
in an msprime
simulation will be around \(2 N_e\),
while in an ms
simulation, the mean time will be around \(0.5\).
Internally, msprime
uses the same algorithm as ms
,
and so the Ne
parameter to the simulate()
function
still acts as a time scaling, and can be set to 0.5
to match many theoretical results,
or to 0.25
to match ms
. Population sizes for individual
demes and for past demographic events are also defined as absolute values, not
scaled by Ne
. All migration rates and growth rates are also per generation.
When running simulations we define the length \(L\) of the sequence in
question using the length
parameter. This defines the coordinate space
within which trees and mutations are defined. \(L\) is a continuous value,
so units are arbitrary, and coordinates can take any value from \(0\) to
\(L\). (So, although we recommend setting the units of length to be
analogous to “bases”, events can occur at fractional positions.)
Mutations occur in an infinite sites process along this sequence,
and mutation rates are specified per generation, per unit of sequence length.
Thus, given the pergeneration mutation rate \(\mu\), the rate of mutation
over the entire sequence in coalescent time units is \(\theta = 4 N_e \mu
L\). It is important to remember these scaling factors when comparing with
analytical results!
Similarly, recombination rates are per unit of sequence length and per
generation in msprime
. Thus, given the per generation crossover rate
\(r\), the overall rate of recombination between the ends of the sequence
in coalescent time units is \(\rho = 4 N_e r L\). Although breakpoints do
not necessarily occur at integer locations, the underlying recombination model
is finite, and the behaviour of a small number of loci can be modelled using
the RecombinationMap
class. However, this is considered an advanced
feature and the majority of cases should be well served with the default
recombination model and number of loci.
Population structure is modelled by specifying a fixed number of demes \(d\), and a \(d \times d\) matrix \(M\) of per generation migration rates. Each element of the matrix \(M_{j,k}\) defines the fraction of population \(j\) that consists of migrants from population \(k\) in each generation. Each deme has an initial absolute population size \(s\) and a per generation exponential growth rate \(\alpha\). The size of a given population at time \(t\) in the past (measured in generations) is therefore given by \(s e^{\alpha t}\). Demographic events that occur in the history of the simulated population alter some aspect of this population configuration at a particular time in the past.
Warning
This parameterisation of recombination, mutation and
migration rates is different to ms, which states these
rates over the entire region and in coalescent time units. The
motivation for this is to allow the user change the size of the simulated
region without having to rescale the recombination and mutation rates,
and to also allow users directly state times and rates in units of
generations. However, the mspms
command line application is
fully ms compatible.
Running simulations¶
The simulate()
function provides the primary interface to running
coalescent simulations in msprime.

msprime.
simulate
(sample_size=None, Ne=1, length=None, recombination_rate=None, recombination_map=None, mutation_rate=None, population_configurations=None, migration_matrix=None, demographic_events=[], samples=None, model=None, record_migrations=False, random_seed=None, mutation_generator=None, num_replicates=None)¶ Simulates the coalescent with recombination under the specified model parameters and returns the resulting
TreeSequence
. Note that Ne is the effective diploid population size (so the effective number of genomes in the population is 2*Ne), butsample_size
is the number of (monoploid) genomes sampled.Parameters:  sample_size (int) – The number of sampled monoploid genomes. If not
specified or None, this defaults to the sum of the subpopulation sample
sizes. Either
sample_size
,population_configurations
orsamples
must be specified.  Ne (float) – The effective (diploid) population size for the reference population. This defaults to 1 if not specified.
 length (float) – The length of the simulated region in bases.
This parameter cannot be used along with
recombination_map
. Defaults to 1 if not specified.  recombination_rate (float) – The rate of recombination per base
per generation. This parameter cannot be used along with
recombination_map
. Defaults to 0 if not specified.  recombination_map (
RecombinationMap
) – The map describing the changing rates of recombination along the simulated chromosome. This parameter cannot be used along with therecombination_rate
orlength
parameters, as these values are encoded within the map. Defaults to a uniform rate as described in therecombination_rate
parameter if not specified.  mutation_rate (float) – The rate of infinite sites
mutations per unit of sequence length per generation.
If not specified, no mutations are generated. This option only
allows for infinite sites mutations with a binary (i.e., 0/1)
alphabet. For more control over the mutational process, please
use the
mutate()
function.  population_configurations (list or None.) – The list of
PopulationConfiguration
instances describing the sampling configuration, relative sizes and growth rates of the populations to be simulated. If this is not specified, a single population with a sample of sizesample_size
is assumed.  migration_matrix (list) – The matrix describing the rates
of migration between all pairs of populations. If \(N\)
populations are defined in the
population_configurations
parameter, then the migration matrix must be an \(N\times N\) matrix with 0 on the diagonal, consisting of \(N\) lists of length \(N\) or an :math`Ntimes N` numpy array.  demographic_events (list) – The list of demographic events to simulate. Demographic events describe changes to the populations in the past. Events should be supplied in nondecreasing order of time in the past. Events with the same time value will be applied sequentially in the order that they were supplied before the simulation algorithm continues with the next time step.
 samples (list) – The list specifying the location and time of
all samples. This parameter may be used to specify historical
samples, and cannot be used in conjunction with the
sample_size
parameter. Each sample is a (population
,time
) pair such that the sample in positionj
in the list of samples is drawn in the specified population at the specfied time. Time is measured in generations ago, as elsewhere.  random_seed (int) – The random seed. If this is None, a random seed will be automatically generated. Valid random seeds must be between 1 and \(2^{32}  1\).
 num_replicates (int) – The number of replicates of the specified
parameters to simulate. If this is not specified or None,
no replication is performed and a
TreeSequence
object returned. Ifnum_replicates
is provided, the specified number of replicates is performed, and an iterator over the resultingTreeSequence
objects returned.
Returns: The
TreeSequence
object representing the results of the simulation if no replication is performed, or an iterator over the independent replicates simulated if thenum_replicates
parameter has been used.Return type: TreeSequence
or an iterator overTreeSequence
replicates.Warning: If using replication, do not store the results of the iterator in a list! For performance reasons, the same underlying object may be used for every TreeSequence returned which will most likely lead to unexpected behaviour.
 sample_size (int) – The number of sampled monoploid genomes. If not
specified or None, this defaults to the sum of the subpopulation sample
sizes. Either
Population structure¶
Population structure is modelled in msprime
by specifying a fixed number of
demes, with the migration rates between those demes defined by a migration
matrix. Each deme has an initial_size
that defines its absolute diploid size at
time zero and a pergeneration growth_rate
which specifies the exponential
growth rate of the subpopulation. We must also define the number of genomes to
sample from each deme. The number of populations and their initial
configuration is defined using the population_configurations
parameter to
simulate()
, which takes a list of PopulationConfiguration
instances. Population IDs are zero indexed, and correspond to their position in
the list.
Samples are drawn sequentially from populations in increasing order of population ID. For example, if we specified an overall sample size of 6, and specify that 2 samples are drawn from population 0 and 4 from population 1, then samples 0 and 1 will be initially located in population 0, and samples 2, 3, 4, and 5 will be drawn from population 2.
Given \(N\) populations, migration matrices are specified using an \(N
\times N\) matrix of demetodeme migration rates. See the documentation for
simulate()
and the Simulation model section for more details on the
migration rates.

class
msprime.
PopulationConfiguration
(sample_size=None, initial_size=None, growth_rate=0.0)¶ The initial configuration of a population (or deme) in a simulation.
Parameters:  sample_size (int) – The number of initial samples that are drawn from this population.
 initial_size (float) – The absolute size of the population at time zero. Defaults to the reference population size \(N_e\).
 growth_rate (float) – The exponential growth rate of the population per generation. Growth rates can be negative. This is zero for a constant population size. Defaults to 0.
Demographic Events¶
Demographic events change some aspect of the population configuration
at some time in the past, and are specified using the demographic_events
parameter to simulate()
. Each element of this list must be an
instance of one of the following demographic events
that are currently supported. Note that all times are measured in
generations, all sizes are absolute (i.e., not relative to \(N_e\)),
and all rates are pergeneration.

class
msprime.
PopulationParametersChange
(time, initial_size=None, growth_rate=None, population=None, population_id=None)¶ Changes the demographic parameters of a population at a given time.
This event generalises the
eg
,eG
,en
andeN
options fromms
. Note that unlikems
we do not automatically set growth rates to zero when the population size is changed.Parameters:  time (float) – The length of time ago at which this event occurred.
 initial_size (float) – The absolute diploid size of the population
at the beginning of the time slice starting at
time
. If None, this is calculated according to the initial population size and growth rate over the preceding time slice.  growth_rate (float) – The new pergeneration growth rate. If None, the growth rate is not changed. Defaults to None.
 population (int) – The ID of the population affected. If
population
is None, the changes affect all populations simultaneously.

class
msprime.
MigrationRateChange
(time, rate, matrix_index=None)¶ Changes the rate of migration to a new value at a specific time.
Parameters:  time (float) – The time at which this event occurs in generations.
 rate (float) – The new pergeneration migration rate.
 matrix_index (tuple) – A tuple of two population IDs descibing
the matrix index of interest. If
matrix_index
is None, all nondiagonal entries of the migration matrix are changed simultaneously.

class
msprime.
MassMigration
(time, source, dest=None, proportion=1.0, destination=None)¶ A mass migration event in which some fraction of the population in one deme simultaneously move to another deme, viewed backwards in time. Each lineage currently present in the source population moves to the destination population with probability equal to
proportion
.This event class generalises the population split (
ej
) and admixture (es
) events fromms
. Note that MassMigrations do not have any side effects on the migration matrix.Parameters:
Debugging demographic models¶
Warning
The DemographyDebugger
class is preliminary, and the API
is likely to change in the future.

class
msprime.
DemographyDebugger
(Ne=1, population_configurations=None, migration_matrix=None, demographic_events=[])¶ A class to facilitate debugging of population parameters and migration rates in the past.

print_history
(output=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF8'>)¶ Prints a summary of the history of the populations.

Variable recombination rates¶

class
msprime.
RecombinationMap
(positions, rates, num_loci=None)¶ A RecombinationMap represents the changing rates of recombination along a chromosome. This is defined via two lists of numbers:
positions
andrates
, which must be of the same length. Given an index j in these lists, the rate of recombination per base per generation isrates[j]
over the intervalpositions[j]
topositions[j + 1]
. Consequently, the first position must be zero, and by convention the last rate value is also required to be zero (although it does not used).Warning
The chromosome is divided into
num_loci
regions of equal recombination distance, between which recombinations occur. This means that if recombination is constant and the genome is lengthn
, thennum_loci=n
will produce breakpoints only at integer values. If recombination rate is not constant, breakpoints will still only occur atn
distinct positions, but these will probably not coincide with thepositions
provided.Parameters:  positions (list) – The positions (in bases) denoting the distinct intervals where recombination rates change. These can be floating point values.
 rates (list) – The list of rates corresponding to the supplied
positions
. Recombination rates are specified per base, per generation.  num_loci (int) – The maximum number of nonrecombining loci in the underlying simulation. By default this is set to the largest possible value, allowing the maximum resolution in the recombination process. However, for a finite sites model this can be set to smaller values.

DEFAULT_NUM_LOCI
= 4294967295¶ The default number of nonrecombining loci in a RecombinationMap.

classmethod
read_hapmap
(filename)¶ Parses the specified file in HapMap format. These files must contain a single header line (which is ignored), and then each subsequent line denotes a position/rate pair. Positions are in units of bases, and recombination rates in centimorgans/Megabase. The first column in this file is ignored, as are subsequence columns after the Position and Rate. A sample of this format is as follows:
Chromosome Position(bp) Rate(cM/Mb) Map(cM) chr1 55550 2.981822 0.000000 chr1 82571 2.082414 0.080572 chr1 88169 2.081358 0.092229 chr1 254996 3.354927 0.439456 chr1 564598 2.887498 1.478148
Parameters: filename (str) – The name of the file to be parsed. This may be in plain text or gzipped plain text.

classmethod
uniform_map
(length, rate, num_loci=None)¶ Returns a
RecombinationMap
instance in which the recombination rate is constant over a chromosome of the specified length. The optionalnum_loci
controls the number of discrete loci in the underlying simulation, and is by default large enough to be effectively be a continuous model.The following map can be used to simulate a true finite locus model with a fixed number of loci
m
:>>> recomb_map = RecombinationMap.uniform_map(m, rate, num_loci=m)
Parameters:
Simulating mutations¶
When running coalescent simulations it’s usually most convenient to use the
mutation_rate
argument to the simulate()
function to throw neutral
mutations down on the trees. However, sometimes we wish to throw mutations
down on an existing tree sequence: for example, if we want to see the outcome
of different random mutational processes on top of a single simulated topology,
or if we have obtained the tree sequence from another program and wish to
overlay neutral mutations on this tree sequence.

class
msprime.
InfiniteSites
(alphabet=0)¶ The “infinitely many sites” mutation model. In this model each mutation corresponds to a unique site, which has a floatingpoint position chose uniformly along the sequence. As a result, each site is associated with exactly one mutation.
By default, the ancestral and derived states in this model are represented by the characters “0” and “1”. Thus, the ancestral state at a site is always “0” and the derived state for a mutation is always “1”. However, by specifying the
alphabet=NUCLEOTIDES
we can generate mutations from the nucleotide characters ACGT. In this case, for each mutation an ancestral state is chosen uniformly from these letters. The derived state is then chosen uniformly from the remaining characters so that the ancestral and derived states are always distinct.

msprime.BINARY == 0
The binary mutation alphabet where ancestral states are always “0” and derived states “1”.

msprime.NUCLEOTIDES == 1
The nucleotides mutation alphabet in which ancestral and derived states are chosen from the characters “A”, “C”, “G” and “T”.

msprime.
mutate
(tree_sequence, rate=None, random_seed=None, model=None, keep=False)¶ Simulates mutations on the specified ancestry and returns the resulting
TreeSequence
. Mutations are generated at the specified rate in measured generations. Mutations are generated under the infinite sites model, and so the rate of new mutations is per unit of sequence length per generation.If a random seed is specified, this is used to seed the random number generator. If the same seed is specified and all other parameters are equal then the same mutations will be generated. If no random seed is specified then one is generated automatically.
If the
model
parameter is specified, this determines the model under which mutations are generated. Currently only theInfiniteSites
mutation model is supported. This parameter is useful if you wish to obtain sequences with letters from the nucleotide alphabet rather than the default 0/1 states. By default mutations from the infinite sites model with a binary alphabet are generated.By default, sites and mutations in the parameter tree sequence are discarded. If the
keep
parameter is true, however, additional mutations are simulated. Under the infinite sites mutation model, all new mutations generated will occur at distinct positions from each other and from any existing mutations (by rejection sampling).Parameters:  tree_sequence (TreeSequence) – The tree sequence onto which we wish to throw mutations.
 rate (float) – The rate of mutation per generation.
 random_seed (int) – The random seed. If this is None, a random seed will be automatically generated. Valid random seeds must be between 1 and \(2^{32}  1\).
 model (MutationModel) – The mutation model to use when generating
mutations. If not specified or None, the
InfiniteSites
mutation model is used.
Returns: The
TreeSequence
object resulting from overlaying mutations on the input tree sequence.Return type:
Using simulation results¶
The TreeSequence
class represents a sequence of correlated trees
output by a simulation. The SparseTree
class represents a single
tree in this sequence.
These classes are the interfaces used to interact with the trees
and mutational information stored in a tree sequence returned from a simulation.
There are also methods for loading data into these objects, either from the native
format using msprime.load()
, or from another sources
using msprime.load_text()
or TableCollection.tree_sequence()
.
Top levelclasses¶

class
msprime.
TreeSequence
¶ A single tree sequence, as defined by the data model. A TreeSequence instance can be created from a set of tables using
TableCollection.tree_sequence()
; or loaded from a set of text files usingload_text()
; or, loaded from a native binary file usingload()
.TreeSequences are immutable. To change the data held in a particular tree sequence, first get the table information as a
TableCollection
instance (usingdump_tables()
), edit those tables using the tables api, and create a new tree sequence usingTableCollection.tree_sequence()
.The
trees()
method iterates over all trees in a tree sequence, and thevariants()
method iterates over all sites and their genotypes.
breakpoints
()¶ Returns an iterator over the breakpoints along the chromosome, including the two extreme points 0 and L. This is equivalent to
>>> [0] + [t.get_interval()[1] for t in self.trees()]
although we do not build an explicit list.
Returns: An iterator over all the breakpoints along the simulated sequence. Return type: iter

dump
(path, zlib_compression=False)¶ Writes the tree sequence to the specified file path.
Parameters:

dump_tables
()¶ A copy of the tables defining this tree sequence.
Returns: A TableCollection
containing all tables underlying the tree sequence.Return type: TableCollection

dump_text
(nodes=None, edges=None, sites=None, mutations=None, provenances=None, precision=6, encoding='utf8', base64_metadata=True)¶ Writes a text representation of the tables underlying the tree sequence to the specified connections.
If Base64 encoding is not used, then metadata will be saved directly, possibly resulting in errors reading the tables back in if metadata includes whitespace.
Parameters:  nodes (stream) – The filelike object (having a .write() method) to write the NodeTable to.
 edges (stream) – The filelike object to write the EdgeTable to.
 sites (stream) – The filelike object to write the SiteTable to.
 mutations (stream) – The filelike object to write the MutationTable to.
 provenances (stream) – The filelike object to write the ProvenanceTable to.
 precision (int) – The number of digits of precision.
 encoding (string) – Encoding used for text representation.
 base64_metadata (bool) – If True, metadata is encoded using Base64 encoding; otherwise, as plain text.

edges
()¶ Returns an iterator over all the edges in this tree sequence. Edges are returned in the order required for a valid tree sequence. So, edges are guaranteed to be ordered such that (a) all parents with a given ID are contiguous; (b) edges are returned in nondescreasing order of parent time ago; (c) within the edges for a given parent, edges are sorted first by child ID and then by left coordinate.
Returns: An iterator over all edges. Return type: iter( Edge
)

first
()¶ Returns the first tree in this
TreeSequence
. To iterate over all trees in the sequence, use thetrees()
method.Currently does not support the extra options for the
trees()
method.Returns: The first tree in this tree sequence. Return type: SparseTree
.

genotype_matrix
()¶ Returns an \(m \times n\) numpy array of the genotypes in this tree sequence, where \(m\) is the number of sites and \(n\) the number of samples. The genotypes are the indexes into the array of
alleles
, as described for theVariant
class. The value 0 always corresponds to the ancestal state, and values > 0 represent distinct derived states.Warning
This method can consume a very large amount of memory! If all genotypes are not needed at once, it is usually better to access them sequentially using the
variants()
iterator.Returns: The full matrix of genotypes. Return type: numpy.ndarray (dtype=np.uint8)

haplotypes
()¶ Returns an iterator over the haplotypes resulting from the trees and mutations in this tree sequence as a string. The iterator returns a total of \(n\) strings, each of which contains \(s\) characters (\(n\) is the sample size returned by
msprime.TreeSequence.num_samples
and \(s\) is the number of sites returned bymsprime.TreeSequence.num_sites
). The first string returned is the haplotype for sample 0, and so on. For a given haplotypeh
, the value ofh[j]
is the observed allelic state at sitej
.See also the
variants()
iterator for sitecentric access to sample genotypes.This method is only supported for singleletter alleles.
Returns: An iterator over the haplotype strings for the samples in this tree sequence. Return type: iter Raises: LibraryError if called on a tree sequence containing multiletter alleles.

individual
(id_)¶ Returns the individual in this tree sequence with the specified ID.
Return type: Individual

individuals
()¶ Returns an iterator over all the individuals in this tree sequence.
Returns: An iterator over all individuals. Return type: iter( Individual
)

migrations
()¶ Returns an iterator over all the migrations in this tree sequence.
Migrations are returned in nondecreasing order of the
time
value.Returns: An iterator over all migrations. Return type: iter( Migration
)

mutation
(id_)¶ Returns the mutation in this tree sequence with the specified ID.
Return type: Mutation

mutations
()¶ Returns an iterator over all the mutations in this tree sequence. Mutations are returned in order of nondecreasing site ID. See the
Mutation
class for details on the available fields for each mutation.The returned iterator is equivalent to iterating over all sites and all mutations in each site, i.e.:
>>> for site in tree_sequence.sites(): >>> for mutation in site.mutations: >>> yield mutation
Returns: An iterator over all mutations in this tree sequence. Return type: iter( Mutation
)

nodes
()¶ Returns an iterator over all the nodes in this tree sequence.
Returns: An iterator over all nodes. Return type: iter( Node
)

num_edges
¶ Returns the number of edges in this tree sequence.
Returns: The number of edges in this tree sequence. Return type: int

num_individuals
¶ Returns the number of individuals in this tree sequence.
Returns: The number of individuals in this tree sequence. Return type: int

num_migrations
¶ Returns the number of migrations in this tree sequence.
Returns: The number of migrations in this tree sequence. Return type: int

num_mutations
¶ Returns the number of mutations in this tree sequence.
Returns: The number of mutations in this tree sequence. Return type: int

num_nodes
¶ Returns the number of nodes in this tree sequence.
Returns: The number of nodes in this tree sequence. Return type: int

num_populations
¶ Returns the number of populations in this tree sequence.
Returns: The number of populations in this tree sequence. Return type: int

num_provenances
¶ Returns the number of provenances in this tree sequence.
Returns: The number of provenances in this tree sequence. Return type: int

num_samples
¶ Returns the number of samples in this tree sequence. This is the number of sample nodes in each tree.
Returns: The number of sample nodes in this tree sequence. Return type: int

num_sites
¶ Returns the number of sites in this tree sequence.
Returns: The number of sites in this tree sequence. Return type: int

num_trees
¶ Returns the number of distinct trees in this tree sequence. This is equal to the number of trees returned by the
trees()
method.Returns: The number of trees in this tree sequence. Return type: int

pairwise_diversity
(samples=None)¶ Returns the value of \(\pi\), the pairwise nucleotide site diversity, the average number of mutations per unit of genome length that differ between a randomly chosen pair of samples. If samples is specified, calculate the diversity within this set.
Note
This method does not currently support sites that have more than one mutation. Using it on such a tree sequence will raise a LibraryError with an “Unsupported operation” message.
Parameters: samples (iterable) – The set of samples within which we calculate the diversity. If None, calculate diversity within the entire sample. Returns: The pairwise nucleotide site diversity. Return type: float

population
(id_)¶ Returns the population in this tree sequence with the specified ID.
Return type: Population

populations
()¶ Returns an iterator over all the populations in this tree sequence.
Returns: An iterator over all populations. Return type: iter( Population
)

provenances
()¶ Returns an iterator over all the provenances in this tree sequence.
Returns: An iterator over all provenances. Return type: iter( Provenance
)

samples
(population=None, population_id=None)¶ Returns an array of the sample node IDs in this tree sequence. If the
population
parameter is specified, only return sample IDs from this population.Parameters: Returns: A numpy array of the node IDs for the samples of interest.
Return type: numpy.ndarray (dtype=np.int32)

sequence_length
¶ Returns the sequence length in this tree sequence. This defines the genomic scale over which tree coordinates are defined. Given a tree sequence with a sequence length \(L\), the constituent trees will be defined over the halfclosed interval \([0, L)\). Each tree then covers some subset of this interval — see
msprime.SparseTree.get_interval()
for details.Returns: The length of the sequence in this tree sequence in bases. Return type: float

simplify
(samples=None, filter_zero_mutation_sites=True, map_nodes=False)¶ Returns a simplified tree sequence that retains only the history of the nodes given in the list
samples
. Ifmap_nodes
is true, also return a numpy array mapping the node IDs in this tree sequence to their node IDs in the simplified tree tree sequence. If a nodeu
is not present in the new tree sequence, the value of this mapping will be NULL_NODE (1).In the returned tree sequence, the node with ID
0
corresponds tosamples[0]
, node1
corresponds tosamples[1]
, and so on. Besides the samples, node IDs in the returned tree sequence are then allocated sequentially in time order.If you wish to simplify a set of tables that do not satisfy all requirements for building a TreeSequence, then use
TableCollection.simplify()
.Parameters:  samples (list) – The list of nodes for which to retain information. This may be a numpy array (or arraylike) object (dtype=np.int32).
 filter_zero_mutation_sites (bool) – If True, remove any sites that have no mutations in the simplified tree sequence. Defaults to True.
 map_nodes (bool) – If True, return a tuple containing the resulting tree sequence and a numpy array mapping node IDs in the current tree sequence to their corresponding node IDs in the returned tree sequence. If False (the default), return only the tree sequence object itself.
Returns: The simplified tree sequence, or (if
map_nodes
is True) a tuple consisting of the simplified tree sequence and a numpy array mapping source node IDs to their corresponding IDs in the new tree sequence.Return type: TreeSequence or a (TreeSequence, numpy.array) tuple

sites
()¶ Returns an iterator over all the sites in this tree sequence. Sites are returned in order of increasing ID (and also position). See the
Site
class for details on the available fields for each site.Returns: An iterator over all sites. Return type: iter( Site
)

tables
¶ A copy of the tables underlying this tree sequence. See also
dump_tables()
.Warning
This propery currently returns a copy of the tables underlying a tree sequence but it may return a readonly view in the future. Thus, if the tables will subsequently be updated, please use the
dump_tables()
method instead as this will always return a new copy of the TableCollection.Returns: A TableCollection
containing all a copy of the tables underlying this tree sequence.Return type: TableCollection

trees
(tracked_samples=None, sample_counts=True, sample_lists=False, tracked_leaves=None, leaf_counts=None, leaf_lists=None)¶ Returns an iterator over the trees in this tree sequence. Each value returned in this iterator is an instance of
SparseTree
.The
sample_counts
andsample_lists
parameters control the features that are enabled for the resulting trees. Ifsample_counts
is True, then it is possible to count the number of samples underneath a particular node in constant time using thenum_samples()
method. Ifsample_lists
is True a more efficient algorithm is used in theSparseTree.samples()
method.The
tracked_samples
parameter can be used to efficiently count the number of samples in a given set that exist in a particular subtree using theSparseTree.get_num_tracked_samples()
method. It is an error to use thetracked_samples
parameter when thesample_counts
flag is False.Warning: Do not store the results of this iterator in a list! For performance reasons, the same underlying object is used for every tree returned which will most likely lead to unexpected behaviour.
Parameters:  tracked_samples (list) – The list of samples to be tracked and
counted using the
SparseTree.get_num_tracked_samples()
method.  sample_counts (bool) – If True, support constant time sample counts
via the
SparseTree.num_samples()
andSparseTree.get_num_tracked_samples()
methods.  sample_lists (bool) – If True, provide more efficient access
to the samples beneath a give node using the
SparseTree.samples()
method.
Returns: An iterator over the sparse trees in this tree sequence.
Return type: iter
 tracked_samples (list) – The list of samples to be tracked and
counted using the

variants
(as_bytes=False)¶ Returns an iterator over the variants in this tree sequence. See the
Variant
class for details on the fields of each returned object. By default thegenotypes
for the variants are numpy arrays, corresponding to indexes into thealleles
array. If theas_bytes
parameter is true, these allelic values are recorded directly into a bytes array.Note
The
as_bytes
parameter is kept as a compatibility option for older code. It is not the recommended way of accessing variant data, and will be deprecated in a later release. Another method will be provided to obtain the allelic states for each site directly.Parameters: as_bytes (bool) – If True, the genotype values will be returned as a Python bytes object. This is useful in certain situations (i.e., directly printing the genotypes) or when numpy is not available. Otherwise, genotypes are returned as a numpy array (the default). Returns: An iterator of all variants this tree sequence. Return type: iter( Variant
)

write_vcf
(output, ploidy=1, contig_id='1')¶ Writes a VCF formatted file to the specified filelike object. If a ploidy value is supplied, allele values are combined among adjacent samples to form a phased genotype of the required ploidy. For example, if we have a ploidy of 2 and a sample of size 6, then we will have 3 diploid samples in the output, consisting of the combined alleles for samples [0, 1], [2, 3] and [4, 5]. If we had alleles 011110 at a particular variant, then we would output the genotypes 01, 11 and 10 in VCF. Sample names are generated by appending the index to the prefix
msp_
such that we would have the sample namesmsp_0
,msp_1
andmsp_2
in the running example.Example usage:
>>> with open("output.vcf", "w") as vcf_file: >>> tree_sequence.write_vcf(vcf_file, 2)
Warning
This output function does not currently use information in the
IndividualTable
, and so will only correctly produce nonhaploid output if the nodes corresponding to each individual are contiguous as described above.Parameters:


class
msprime.
SparseTree
¶ A SparseTree is a single tree in a
TreeSequence
. The SparseTree implementation differs from most tree implementations by using integer node IDs to refer to nodes rather than objects. Thus, when we wish to find the parent of the node with ID ‘0’, we usetree.parent(0)
, which returns another integer. If ‘0’ does not have a parent in the current tree (e.g., if it is a root), then the special valueNULL_NODE
(\(1\)) is returned. The children of a node are found using thechildren()
method. To obtain information about a particular node, one may either usetree.tree_sequence.node(u)
to obtain the correspondingNode
instance, or use thetime()
orpopulation()
shorthands. Tree traversals in various orders is possible using theSparseTree.nodes()
iterator.Sparse trees are not intended to be instantiated directly, and are obtained as part of a
TreeSequence
using thetrees()
method.
branch_length
(u)¶ Returns the length of the branch (in generations) joining the specified node to its parent. This is equivalent to
>>> tree.time(tree.parent(u))  tree.time(u)
Note that this is not related to the value returned by
length
, which describes the length of the interval covered by the tree in genomic coordinates.Parameters: u (int) – The node of interest. Returns: The branch length from u to its parent. Return type: float

children
(u)¶ Returns the children of the specified node
u
as a tuple of integer node IDs. Ifu
is a leaf, return the empty tuple.Parameters: u (int) – The node of interest. Returns: The children of u
as a tuple of integersReturn type: tuple(int)

draw
(path=None, width=None, height=None, node_labels=None, node_colours=None, mutation_labels=None, mutation_colours=None, format=None)¶ Returns a drawing of this tree.
When working in a Jupyter notebook, use the
IPython.display.SVG
function to display the SVG output from this function inline in the notebook:>>> SVG(tree.draw())
The unicode format uses unicode box drawing characters to render the tree. This allows rendered trees to be printed out to the terminal:
>>> print(tree.draw(format="unicode")) 6 ┏━┻━┓ ┃ 5 ┃ ┏━┻┓ ┃ ┃ 4 ┃ ┃ ┏┻┓ 3 0 1 2
The
node_labels
argument allows the user to specify custom labels for nodes, or no labels at all:>>> print(tree.draw(format="unicode", node_labels={})) ┃ ┏━┻━┓ ┃ ┃ ┃ ┏━┻┓ ┃ ┃ ┃ ┃ ┃ ┏┻┓ ┃ ┃ ┃ ┃
Parameters:  path (str) – The path to the file to write the output. If None, do not write to file.
 width (int) – The width of the image in pixels. If not specified, either defaults to the minimum size required to depict the tree (text formats) or 200 pixels.
 height (int) – The height of the image in pixels. If not specified, either defaults to the minimum size required to depict the tree (text formats) or 200 pixels.
 node_labels (map) – If specified, show custom labels for the nodes that are present in the map. Any nodes not specified in the map will not have a node label.
 node_colours (map) – If specified, show custom colours for nodes. (Only supported in the SVG format.)
 format (str) – The format of the returned image. Currently supported are ‘svg’, ‘ascii’ and ‘unicode’.
Returns: A representation of this tree in the requested format.
Return type:

index
¶ Returns the index this tree occupies in the parent tree sequence. This index is zero based, so the first tree in the sequence has index 0.
Returns: The index of this tree. Return type: int

interval
¶ Returns the coordinates of the genomic interval that this tree represents the history of. The interval is returned as a tuple \((l, r)\) and is a halfopen interval such that the left coordinate is inclusive and the right coordinate is exclusive. This tree therefore applies to all genomic locations \(x\) such that \(l \leq x < r\).
Returns: A tuple (l, r) representing the leftmost (inclusive) and rightmost (exclusive) coordinates of the genomic region covered by this tree. Return type: tuple

is_internal
(u)¶ Returns True if the specified node is not a leaf. A node is internal if it has one or more children in the current tree.
Parameters: u (int) – The node of interest. Returns: True if u is not a leaf node. Return type: bool

is_leaf
(u)¶ Returns True if the specified node is a leaf. A node \(u\) is a leaf if it has zero children.
Parameters: u (int) – The node of interest. Returns: True if u is a leaf node. Return type: bool

is_sample
(u)¶ Returns True if the specified node is a sample. A node \(u\) is a sample if it has been marked as a sample in the parent tree sequence.
Parameters: u (int) – The node of interest. Returns: True if u is a sample. Return type: bool

leaves
(u=None)¶ Returns an iterator over all the leaves in this tree that are underneath the specified node. If u is not specified, return all leaves in the tree.
Parameters: u (int) – The node of interest. Returns: An iterator over all leaves in the subtree rooted at u. Return type: iterator

length
¶ Returns the length of the genomic interval that this tree represents. This is defined as \(r  l\), where \((l, r)\) is the genomic interval returned by
interval
.Returns: The length of the genomic interval covered by this tree. Return type: int

mrca
(u, v)¶ Returns the most recent common ancestor of the specified nodes.
Parameters: Returns: The most recent common ancestor of u and v.
Return type:

mutations
()¶ Returns an iterator over all the mutations in this tree. Mutations are returned in order of nondecreasing site ID. See the
Mutation
class for details on the available fields for each mutation.The returned iterator is equivalent to iterating over all sites and all mutations in each site, i.e.:
>>> for site in tree.sites(): >>> for mutation in site.mutations: >>> yield mutation
Returns: An iterator over all mutations in this tree. Return type: iter( Mutation
)

newick
(precision=14, root=None, node_labels=None)¶ Returns a newick encoding of this tree. If the
root
argument is specified, return a representation of the specified subtree, otherwise the full tree is returned. If the tree has multiple roots then seperate newick strings for each rooted subtree must be found (i.e., we do not attempt to concatenate the different trees).By default, leaf nodes are labelled with their numerical ID + 1, and internal nodes are not labelled. Arbitrary node labels can be specified using the
node_labels
argument, which maps node IDs to the desired labels.Warning
Node labels are not Newick escaped, so care must be taken to provide labels that will not break the encoding.
Parameters:  precision (int) – The numerical precision with which branch lengths are printed.
 root (int) – If specified, return the tree rooted at this node.
 node_labels (map) – If specified, show custom labels for the nodes that are present in the map. Any nodes not specified in the map will not have a node label.
Returns: A newick representation of this tree.
Return type:

nodes
(root=None, order='preorder')¶ Returns an iterator over the nodes in this tree. If the root parameter is provided, iterate over the nodes in the subtree rooted at this node. If this is None, iterate over all nodes. If the order parameter is provided, iterate over the nodes in required tree traversal order.
Parameters: Returns: An iterator over the nodes in the tree in some traversal order.
Return type: iterator

num_mutations
¶ Returns the total number of mutations across all sites on this tree.
Returns: The total number of mutations over all sites on this tree. Return type: int

num_roots
¶ The number of roots in this tree, as defined in the
roots
attribute.Requires O(number of roots) time.
Return type: int

num_samples
(u=None)¶ Returns the number of samples in this tree underneath the specified node (including the node itself). If u is not specified return the total number of samples in the tree.
If the
TreeSequence.trees()
method is called withsample_counts=True
this method is a constant time operation. If not, a slower traversal based algorithm is used to count the samples.Parameters: u (int) – The node of interest. Returns: The number of samples in the subtree rooted at u. Return type: int

num_sites
¶ Returns the number of sites on this tree.
Returns: The number of sites on this tree. Return type: int

num_tracked_samples
(u=None)¶ Returns the number of samples in the set specified in the
tracked_samples
parameter of theTreeSequence.trees()
method underneath the specified node. If the input node is not specified, return the total number of tracked samples in the tree.This is a constant time operation.
Parameters: u (int) – The node of interest. Returns: The number of samples within the set of tracked samples in the subtree rooted at u. Return type: int Raises: RuntimeError – if the TreeSequence.trees()
method is not called withsample_counts=True
.

parent
(u)¶ Returns the parent of the specified node. Returns the
NULL_NODE
if u is the root or is not a node in the current tree.Parameters: u (int) – The node of interest. Returns: The parent of u. Return type: int

population
(u)¶ Returns the population associated with the specified node. Equivalent to
tree.tree_sequence.node(u).population
.Parameters: u (int) – The node of interest. Returns: The ID of the population associated with node u. Return type: int

root
¶ The root of this tree. If the tree contains multiple roots, a ValueError is raised indicating that the
roots
attribute should be used instead.Returns: The root node. Return type: int Raises: ValueError
if this tree contains more than one root.

roots
¶ The list of roots in this tree. A root is defined as a unique endpoint of the paths starting at samples. We can define the set of roots as follows:
roots = set() for u in tree_sequence.samples(): while tree.parent(u) != msprime.NULL_NODE: u = tree.parent(u) roots.add(u) # roots is now the set of all roots in this tree. assert sorted(roots) == sorted(tree.roots)
The roots of the tree are returned in a list, in no particular order.
Requires O(number of roots) time.
Returns: The list of roots in this tree. Return type: list

sample_size
¶ Returns the sample size for this tree. This is the number of sample nodes in the tree.
Returns: The number of sample nodes in the tree. Return type: int

samples
(u=None)¶ Returns an iterator over all the samples in this tree that are underneath the specified node. If u is a sample, it is included in the returned iterator. If u is not specified, return all samples in the tree.
If the
TreeSequence.trees()
method is called withsample_lists=True
, this method uses an efficient algorithm to find the samples. If not, a simple traversal based method is used.Parameters: u (int) – The node of interest. Returns: An iterator over all samples in the subtree rooted at u. Return type: iterator

sites
()¶ Returns an iterator over all the sites in this tree. Sites are returned in order of increasing ID (and also position). See the
Site
class for details on the available fields for each site.Returns: An iterator over all sites in this tree. Return type: iter( Site
)

time
(u)¶ Returns the time of the specified node in generations. Equivalent to
tree.tree_sequence.node(u).time
.Parameters: u (int) – The node of interest. Returns: The time of u. Return type: float

tmrca
(u, v)¶ Returns the time of the most recent common ancestor of the specified nodes. This is equivalent to:
>>> tree.time(tree.mrca(u, v))
Parameters: Returns: The time of the most recent common ancestor of u and v.
Return type:

total_branch_length
¶ Returns the sum of all the branch lengths in this tree (in units of generations). This is equivalent to
>>> sum( >>> tree.branch_length(u) for u in tree.nodes() >>> if u not in self.roots)
Returns: The sum of all the branch lengths in this tree. Return type: float

tree_sequence
¶ Returns the tree sequence that this tree is from.
Returns: The parent tree sequence for this tree. Return type: TreeSequence

Constants¶
These constants are used in TreeSequence
and SparseTree
instances to define special values of various variables.

msprime.NULL_NODE == 1
Special reserved value, representing the null node. If the parent of a given node is null, then this node is either a root (the ancestor of one or more samples), or the node is not present in the current tree.

msprime.NULL_POPULATION == 1
Special reserved value, representing the null population ID. This value is returned if the population associated with a particular node is not defined, or population information was not available in the underlying tree sequence.

msprime.NULL_INDIVIDUAL == 1
Special reserved value, representing the null individual ID. This value is returned if the individual associated with a particular node is not defined, or individual information was not available in the underlying tree sequence.

msprime.NULL_MUTATION == 1
Special reserved value, representing the null mutation ID. If there is a single mutation at a site, or if a mutation at a given site does not have an ancestal mutations it inherited from, this is the value returned by
mutation.parent
. See alsoMutation
.

msprime.FORWARD == 1
Constant representing the forward direction of travel (i.e., increasing genomic coordinate values).

msprime.REVERSE == 1
Constant representing the reverse direction of travel (i.e., decreasing genomic coordinate values).
Simple container classes¶
These classes are simple shallow containers representing the entities defined
in the Data model. These classes are not intended to be instantiated
directly, but are the return types for the various iterators provided by the
TreeSequence
and SparseTree
classes.

class
msprime.
Individual
¶ An individual in a tree sequence. Since nodes correspond to genomes, individuals are associated with a collection of nodes (e.g., two nodes per diploid). See Nodes, Genomes, or Individuals? for more discussion of this distinction.
Modifying the attributes in this class will have no effect on the underlying tree sequence data.
Variables:  id (int) – The integer ID of this individual. Varies from 0 to
TreeSequence.num_individuals
 1.  flags (int) – The bitwise flags for this individual.
 location (numpy.ndarray) – The spatial location of this individual as a numpy array. The location is an empty array if no spatial location is defined.
 nodes – The IDs of the nodes that are associated with this individual as a numpy array (dtype=np.int32). If no nodes are associated with the individual this array will be empty.
 metadata (bytes) – The metadata for this individual.
 id (int) – The integer ID of this individual. Varies from 0 to

class
msprime.
Node
¶ A node in a tree sequence, corresponding to a single genome. The
time
andpopulation
are attributes of theNode
, rather than theIndividual
, as discussed in Nodes, Genomes, or Individuals?.Modifying the attributes in this class will have no effect on the underlying tree sequence data.
Variables:  id (int) – The integer ID of this node. Varies from 0 to
TreeSequence.num_nodes
 1.  flags (int) – The bitwise flags for this node.
 time (float) – The birth time of this node.
 population (int) – The integer ID of the population that this node was born in.
 individual (int) – The integer ID of the individual that this node was a part of.
 metadata (bytes) – The metadata for this node.
 id (int) – The integer ID of this node. Varies from 0 to

class
msprime.
Edge
¶ An edge in a tree sequence.
Modifying the attributes in this class will have no effect on the underlying tree sequence data.
Variables:  left (float) – The left coordinate of this edge.
 right (float) – The right coordinate of this edge.
 parent (int) – The integer ID of the parent node for this edge.
To obtain further information about a node with a given ID, use
TreeSequence.node()
.  child (int) – The integer ID of the child node for this edge.
To obtain further information about a node with a given ID, use
TreeSequence.node()
.

class
msprime.
Site
¶ A site in a tree sequence.
Modifying the attributes in this class will have no effect on the underlying tree sequence data.
Variables:  id (int) – The integer ID of this site. Varies from 0 to
TreeSequence.num_sites
 1.  position (float) – The floating point location of this site in genome coordinates.
Ranges from 0 (inclusive) to
TreeSequence.sequence_length
(exclusive).  ancestral_state (str) – The ancestral state at this site (i.e., the state inherited by nodes, unless mutations occur).
 metadata (bytes) – The metadata for this site.
 mutations (list[
Mutation
]) – The list of mutations at this site. Mutations within a site are returned in the order they are specified in the underlyingMutationTable
.
 id (int) – The integer ID of this site. Varies from 0 to

class
msprime.
Mutation
¶ A mutation in a tree sequence.
Modifying the attributes in this class will have no effect on the underlying tree sequence data.
Variables:  id (int) – The integer ID of this mutation. Varies from 0 to
TreeSequence.num_mutations
 1.  site (int) – The integer ID of the site that this mutation occurs at. To obtain
further information about a site with a given ID use
TreeSequence.site()
.  node (int) – The integer ID of the first node that inherits this mutation.
To obtain further information about a node with a given ID, use
TreeSequence.node()
.  derived_state (str) – The derived state for this mutation. This is the state inherited by nodes in the subtree rooted at this mutation’s node, unless another mutation occurs.
 parent (int) – The integer ID of this mutation’s parent mutation. When multiple
mutations occur at a site along a path in the tree, mutations must
record the mutation that is immediately above them. If the mutation does
not have a parent, this is equal to the
NULL_MUTATION
(1). To obtain further information about a mutation with a given ID, useTreeSequence.mutation()
.  metadata (bytes) – The metadata for this site.
 id (int) – The integer ID of this mutation. Varies from 0 to

class
msprime.
Variant
¶ A variant is represents the observed variation among the samples for a given site. A variant consists (a) of a reference to the
Site
instance in question; (b) the alleles that may be observed at the samples for this site; and (c) the genotypes mapping sample IDs to the observed alleles.Each element in the
alleles
tuple is a string, representing the actual observed state for a given sample. The first element of this tuple is guaranteed to be the same as the site’sancestral_state
value. The list of alleles is also guaranteed not to contain any duplicates. However, allelic values may be listed that are not referred to by any samples. For example, if we have a site that is fixed for the derived state (i.e., we have a mutation over the tree root), all genotypes will be 1, but the alleles list will be equal to('0', '1')
. Other than the ancestral state being the first allele, the alleles are listed in no particular order, and the ordering should not be relied upon.The
genotypes
represent the observed allelic states for each sample, such thatvar.alleles[var.genotypes[j]]
gives the string allele for sample IDj
. Thus, the elements of the genotypes array are indexes into thealleles
list. The genotypes are provided in this way via a numpy array to enable efficient calculations.Modifying the attributes in this class will have no effect on the underlying tree sequence data.
Variables:  site (
Site
) – The site object for this variant.  alleles (tuple(str)) – A tuple of the allelic values that may be observed at the samples at the current site. The first element of this tuple is always the sites’s ancestral state.
 genotypes (numpy.ndarray) – An array of indexes into the list
alleles
, giving the state of each sample at the current site.
 site (

class
msprime.
Migration
¶ A migration in a tree sequence.
Modifying the attributes in this class will have no effect on the underlying tree sequence data.
Variables:  left (float) – The left end of the genomic interval covered by this migration (inclusive).
 right (float) – The right end of the genomic interval covered by this migration (exclusive).
 node (int) – The integer ID of the node involved in this migration event.
To obtain further information about a node with a given ID, use
TreeSequence.node()
.  source (int) – The source population ID.
 dest (int) – The destination population ID.
 time (float) – The time at which this migration occured at.

class
msprime.
Population
¶ A population in a tree sequence.
Modifying the attributes in this class will have no effect on the underlying tree sequence data.
Variables:  id (int) – The integer ID of this population. Varies from 0 to
TreeSequence.num_populations
 1.  metadata (bytes) – The metadata for this population.
 id (int) – The integer ID of this population. Varies from 0 to
Loading data¶
There are several methods for loading data into a TreeSequence
instance. The simplest and most convenient is the use the msprime.load()
function to load a tree sequence file. For small
scale data and debugging, it is often convenient to use the
msprime.load_text()
to read data in the text file format. The TableCollection.tree_sequence()
function
efficiently creates a TreeSequence
object from a set of tables
using the Tables API.

msprime.
load
(path)¶ Loads a tree sequence from the specified file path. This file must be in the tree sequence file format produced by the
TreeSequence.dump()
method.Parameters: path (str) – The file path of the .trees
file containing the tree sequence we wish to load.Returns: The tree sequence object containing the information stored in the specified file path. Return type: msprime.TreeSequence

msprime.
load_text
(nodes, edges, sites=None, mutations=None, sequence_length=0, strict=True, encoding='utf8', base64_metadata=True)¶ Parses the tree sequence data from the specified filelike objects, and returns the resulting
TreeSequence
object. The format for these files is documented in the Text file formats section, and is produced by theTreeSequence.dump_text()
method. Further properties required for an input tree sequence are described in the Valid tree sequence requirements section. This method is intended as a convenient interface for importing external data into msprime; the binary file format using bymsprime.load()
is many times more efficient than this text format.The
nodes
andedges
parameters are mandatory and must be filelike objects containing text with whitespace delimited columns, parsable byparse_nodes()
andparse_edges()
, respectively.sites
andmutations
are optional, and must be parsable byparse_sites()
andparse_mutations()
, respectively.TODO: there is no method to parse the remaining tables at present, so only tree sequences not requiring Population and Individual tables can be loaded. This will be fixed: https://github.com/tskitdev/msprime/issues/498
The
sequence_length
parameter determines theTreeSequence.sequence_length
of the returned tree sequence. If it is 0 or not specified, the value is taken to be the maximum right coordinate of the input edges. This parameter is useful in degenerate situations (such as when there are zero edges), but can usually be ignored.The
strict
parameter controls the field delimiting algorithm that is used. Ifstrict
is True (the default), we require exactly one tab character separating each field. Ifstrict
is False, a more relaxed whitespace delimiting algorithm is used, such that any run of whitespace is regarded as a field separator. In most situations,strict=False
is more convenient, but it can lead to error in certain situations. For example, if a deletion is encoded in the mutation table this will not be parseable whenstrict=False
.After parsing the tables,
sort_tables()
is called to ensure that the loaded tables satisfy the tree sequence ordering requirements. Note that this may result in the IDs of various entities changing from their positions in the input file.Parameters:  nodes (stream) – The filelike object containing text describing a
NodeTable
.  edges (stream) – The filelike object containing text
describing an
EdgeTable
.  sites (stream) – The filelike object containing text describing a
SiteTable
.  mutations (stream) – The filelike object containing text
describing a
MutationTable
.  sequence_length (float) – The sequence length of the returned tree sequence. If not supplied or zero this will be inferred from the set of edges.
 strict (bool) – If True, require strict tab delimiting (default). If False, a relaxed whitespace splitting algorithm is used.
 encoding (string) – Encoding used for text representation.
 base64_metadata (bool) – If True, metadata is encoded using Base64 encoding; otherwise, as plain text.
Returns: The tree sequence object containing the information stored in the specified file paths.
Return type:  nodes (stream) – The filelike object containing text describing a
Calculating statistics¶
The msprime
API provides methods for efficiently calculating
population genetics statistics from a given TreeSequence
.

class
msprime.
LdCalculator
(tree_sequence)¶ Class for calculating linkage disequilibrium coefficients between pairs of mutations in a
TreeSequence
. This class requires the numpy library.This class supports multithreaded access using the Python
threading
module. Separate instances ofLdCalculator
referencing the same tree sequence can operate in parallel in multiple threads. See the Working with threads section in the Tutorial for an example of how use multiple threads to calculate LD values efficiently.Note
This class does not currently support sites that have more than one mutation. Using it on such a tree sequence will raise a LibraryError with an “Unsupported operation” message.
Parameters: tree_sequence (TreeSequence) – The tree sequence containing the mutations we are interested in. 
r2
(a, b)¶ Returns the value of the \(r^2\) statistic between the pair of mutations at the specified indexes. This method is not an efficient method for computing large numbers of pairwise; please use either
r2_array()
orr2_matrix()
for this purpose.Parameters: Returns: The value of \(r^2\) between the mutations at indexes
a
andb
.Return type:

r2_array
(a, direction=1, max_mutations=None, max_distance=None)¶ Returns the value of the \(r^2\) statistic between the focal mutation at index \(a\) and a set of other mutations. The method operates by starting at the focal mutation and iterating over adjacent mutations (in either the forward or backwards direction) until either a maximum number of other mutations have been considered (using the
max_mutations
parameter), a maximum distance in sequence coordinates has been reached (using themax_distance
parameter) or the start/end of the sequence has been reached. For every mutation \(b\) considered, we then insert the value of \(r^2\) between \(a\) and \(b\) at the corresponding index in an array, and return the entire array. If the returned array is \(x\) anddirection
ismsprime.FORWARD
then \(x[0]\) is the value of the statistic for \(a\) and \(a + 1\), \(x[1]\) the value for \(a\) and \(a + 2\), etc. Similarly, ifdirection
ismsprime.REVERSE
then \(x[0]\) is the value of the statistic for \(a\) and \(a  1\), \(x[1]\) the value for \(a\) and \(a  2\), etc.Parameters:  a (int) – The index of the focal mutation.
 direction (int) – The direction in which to travel when
examining other mutations. Must be either
msprime.FORWARD
ormsprime.REVERSE
. Defaults tomsprime.FORWARD
.  max_mutations (int) – The maximum number of mutations to return \(r^2\) values for. Defaults to as many mutations as possible.
 max_distance (float) – The maximum absolute distance between the focal mutation and those for which \(r^2\) values are returned.
Returns: An array of double precision floating point values representing the \(r^2\) values for mutations in the specified direction.
Return type: Warning: For efficiency reasons, the underlying memory used to store the returned array is shared between calls. Therefore, if you wish to store the results of a single call to
get_r2_array()
for later processing you must take a copy of the array!

r2_matrix
()¶ Returns the complete \(m \times m\) matrix of pairwise \(r^2\) values in a tree sequence with \(m\) mutations.
Returns: An 2 dimensional square array of double precision floating point values representing the \(r^2\) values for all pairs of mutations. Return type: numpy.ndarray

Tables API¶
The tables API provides an efficient way of working
with and interchanging tree sequence data. Each table
class (e.g, NodeTable
, EdgeTable
) has a specific set of
columns with fixed types, and a set of methods for setting and getting the data
in these columns. The number of rows in the table t
is given by len(t)
.
Each table supports accessing the data either by row or column. To access the
row j
in table t
simply use t[j]
. The value returned by such an
access is an instance of collections.namedtuple()
, and therefore supports
either positional or named attribute access. To access the data in
a column, we can use standard attribute access which will return a numpy array
of the data. For example:
>>> import msprime
>>> t = msprime.EdgeTable()
>>> t.add_row(left=0, right=1, parent=10, child=11)
0
>>> t.add_row(left=1, right=2, parent=9, child=11)
1
>>> print(t)
id left right parent child
0 0.00000000 1.00000000 10 11
1 1.00000000 2.00000000 9 11
>>> t[0]
EdgeTableRow(left=0.0, right=1.0, parent=10, child=11)
>>> t[1]
EdgeTableRow(left=1.0, right=2.0, parent=9, child=11)
>>> t.left
array([ 0., 1.])
>>> t.parent
array([10, 9], dtype=int32)
>>> len(t)
2
>>>
Tables also support the pickle
protocol, and so can be easily
serialised and deserialised (for example, when performing parallel
computations using the multiprocessing
module).
>>> serialised = pickle.dumps(t)
>>> t2 = pickle.loads(serialised)
>>> print(t2)
id left right parent child
0 0.00000000 1.00000000 10 11
1 1.00000000 2.00000000 9 11
However, pickling will not be as efficient as storing tables in the native format.
Tables support the equality operator ==
based on the data
held in the columns:
>>> t == t2
True
>>> t is t2
False
>>> t2.add_row(0, 1, 2, 3)
2
>>> print(t2)
id left right parent child
0 0.00000000 1.00000000 10 11
1 1.00000000 2.00000000 9 11
2 0.00000000 1.00000000 2 3
>>> t == t2
False
Text columns¶
As described in the Encoding ragged columns, working with variable length columns is somewhat more involved. Columns encoding text data store the encoded bytes of the flattened strings, and the offsets into this column in two separate arrays.
Consider the following example:
>>> t = msprime.SiteTable()
>>> t.add_row(0, "A")
>>> t.add_row(1, "BB")
>>> t.add_row(2, "")
>>> t.add_row(3, "CCC")
>>> print(t)
id position ancestral_state metadata
0 0.00000000 A
1 1.00000000 BB
2 2.00000000
3 3.00000000 CCC
>>> t[0]
SiteTableRow(position=0.0, ancestral_state='A', metadata=b'')
>>> t[1]
SiteTableRow(position=1.0, ancestral_state='BB', metadata=b'')
>>> t[2]
SiteTableRow(position=2.0, ancestral_state='', metadata=b'')
>>> t[3]
SiteTableRow(position=3.0, ancestral_state='CCC', metadata=b'')
Here we create a SiteTable
and add four rows, each with a different
ancestral_state
. We can then access this information from each
row in a straightforward manner. Working with the data in the columns
is a little trickier, however:
>>> t.ancestral_state
array([65, 66, 66, 67, 67, 67], dtype=int8)
>>> t.ancestral_state_offset
array([0, 1, 3, 3, 6], dtype=uint32)
>>> msprime.unpack_strings(t.ancestral_state, t.ancestral_state_offset)
['A', 'BB', '', 'CCC']
Here, the ancestral_state
array is the UTF8 encoded bytes of the flattened
strings, and the ancestral_state_offset
is the offset into this array
for each row. The unpack_strings()
function, however, is a convient
way to recover the original strings from this encoding. We can also use the
pack_strings()
to insert data using this approach:
>>> a, off = msprime.pack_strings(["0", "12", ""])
>>> t.set_columns(position=[0, 1, 2], ancestral_state=a, ancestral_state_offset=off)
>>> print(t)
id position ancestral_state metadata
0 0.00000000 0
1 1.00000000 12
2 2.00000000
When inserting many rows with standard infinite sites mutations (i.e.,
ancestral state is “0”), it is more efficient to construct the
numpy arrays directly than to create a list of strings and use
pack_strings()
. When doing this, it is important to note that
it is the encoded byte values that are stored; by default, we
use UTF8 (which corresponds to ASCII for simple printable characters).:
>>> t_s = msprime.SiteTable()
>>> m = 10
>>> a = ord("0") + np.zeros(m, dtype=np.int8)
>>> off = np.arange(m + 1, dtype=np.uint32)
>>> t_s.set_columns(position=np.arange(m), ancestral_state=a, ancestral_state_offset=off)
>>> print(t_s)
id position ancestral_state metadata
0 0.00000000 0
1 1.00000000 0
2 2.00000000 0
3 3.00000000 0
4 4.00000000 0
5 5.00000000 0
6 6.00000000 0
7 7.00000000 0
8 8.00000000 0
9 9.00000000 0
>>> t_s.ancestral_state
array([48, 48, 48, 48, 48, 48, 48, 48, 48, 48], dtype=int8)
>>> t_s.ancestral_state_offset
array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10], dtype=uint32)
Here we create 10 sites at regular positions, each with ancestral state equal to
“0”. Note that we use ord("0")
to get the ASCII code for “0” (48), and create
10 copies of this by adding it to an array of zeros. We have done this for
illustration purposes: it is equivalent (though slower for large examples) to do
a, off = msprime.pack_strings(["0"] * m)
.
Mutations can be handled similarly:
>>> t_m = msprime.MutationTable()
>>> site = np.arange(m, dtype=np.int32)
>>> d, off = msprime.pack_strings(["1"] * m)
>>> node = np.zeros(m, dtype=np.int32)
>>> t_m.set_columns(site=site, node=node, derived_state=d, derived_state_offset=off)
>>> print(t_m)
id site node derived_state parent metadata
0 0 0 1 1
1 1 0 1 1
2 2 0 1 1
3 3 0 1 1
4 4 0 1 1
5 5 0 1 1
6 6 0 1 1
7 7 0 1 1
8 8 0 1 1
9 9 0 1 1
>>>
Binary columns¶
Columns storing binary data take the same approach as
Text columns to encoding
variable length data.
The difference between the two is
only raw bytes
values are accepted: no character encoding or
decoding is done on the data. Consider the following example:
>>> t = msprime.NodeTable()
>>> t.add_row(metadata=b"raw bytes")
>>> t.add_row(metadata=pickle.dumps({"x": 1.1}))
>>> t[0].metadata
b'raw bytes'
>>> t[1].metadata
b'\x80\x03}q\x00X\x01\x00\x00\x00xq\x01G?\xf1\x99\x99\x99\x99\x99\x9as.'
>>> pickle.loads(t[1].metadata)
{'x': 1.1}
>>> print(t)
id flags population time metadata
0 0 1 0.00000000000000 cmF3IGJ5dGVz
1 0 1 0.00000000000000 gAN9cQBYAQAAAHhxAUc/8ZmZmZmZmnMu
>>> t.metadata
array([ 114, 97, 119, 32, 98, 121, 116, 101, 115, 128, 3,
125, 113, 0, 88, 1, 0, 0, 0, 120, 113, 1,
71, 63, 15, 103, 103, 103, 103, 103, 102, 115, 46], dtype=int8)
>>> t.metadata_offset
array([ 0, 9, 33], dtype=uint32)
Here we add two rows to a NodeTable
, with different
metadata. The first row contains a simple
byte string, and the second contains a Python dictionary serialised using
pickle
. We then show several different (and seemingly incompatible!)
different views on the same data.
When we access the data in a row (e.g., t[0].metadata
) we are returned
a Python bytes object containing precisely the bytes that were inserted.
The pickled dictionary is encoded in 24 bytes containing unprintable
characters, and when we unpickle it using pickle.loads()
, we obtain
the original dictionary.
When we print the table, however, we see some data which is seemingly unrelated to the original contents. This is because the binary data is base64 encoded to ensure that it is printsafe (and doesn’t break your terminal). (See the Metadata section for more information on the use of base64 encoding.).
Finally, when we print the metadata
column, we see the raw byte values
encoded as signed integers. As for Text columns,
the metadata_offset
column encodes the offsets into this array. So, we
see that the first metadata value is 9 bytes long and the second is 24.
The pack_bytes()
and unpack_bytes()
functions are also useful
for encoding data in these columns.
Table classes¶
This section describes the methods and variables available for each table class. For description and definition of each table’s meaning and use, see the table definitions.

class
msprime.
IndividualTable
¶ A table defining the individuals in a tree sequence. Note that although each Individual has associated nodes, reference to these is not stored in the individual table, but rather reference to the individual is stored for each node in the
NodeTable
. This is similar to the way in which the relationship between sites and mutations is modelled.Warning: The numpy arrays returned by table attribute accesses are copies of the underlying data. In particular, this means that you cannot edit the values in the columns by updating the attribute arrays.
NOTE: this behaviour may change in future.
Variables:  flags (numpy.ndarray, dtype=np.uint32) – The array of flags values.
 location (numpy.ndarray, dtype=np.float64) – The flattened array of floating point location values. See Encoding ragged columns for more details.
 location_offset (numpy.ndarray, dtype=np.uint32) – The array of offsets into the location column. See Encoding ragged columns for more details.
 metadata (numpy.ndarray, dtype=np.int8) – The flattened array of binary metadata values. See Binary columns for more details.
 metadata_offset (numpy.ndarray, dtype=np.uint32) – The array of offsets into the metadata column. See Binary columns for more details.

add_row
(flags=0, location=None, metadata=None)¶ Adds a new row to this
IndividualTable
and returns the ID of the corresponding individual.Parameters:  flags (int) – The bitwise flags for the new node.
 location (arraylike) – A list of numeric values or onedimensional numpy array describing the location of this individual. If not specified or None, a zerodimensional location is stored.
 metadata (bytes) – The binaryencoded metadata for the new node. If not specified or None, a zerolength byte string is stored.
Returns: The ID of the newly added node.
Return type:

append_columns
(flags, location=None, location_offset=None, metadata=None, metadata_offset=None)¶ Appends the specified arrays to the end of the columns in this
IndividualTable
. This allows many new rows to be added at once.The
flags
array is mandatory and defines the number of extra individuals to add to the table. Thelocation
andlocation_offset
parameters must be supplied together, and meet the requirements for Encoding ragged columns. Themetadata
andmetadata_offset
parameters must be supplied together, and meet the requirements for Encoding ragged columns. See Binary columns for more information.Parameters:  flags (numpy.ndarray, dtype=np.uint32) – The bitwise flags for each individual. Required.
 location (numpy.ndarray, dtype=np.float64) – The flattened location array. Must be specified along
with
location_offset
. If not specified or None, an empty location value is stored for each individual.  location_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the
location
array.  metadata (numpy.ndarray, dtype=np.int8) – The flattened metadata array. Must be specified along
with
metadata_offset
. If not specified or None, an empty metadata value is stored for each individual.  metadata_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the
metadata
array.

clear
()¶ Deletes all rows in this table.

copy
()¶ Returns a deep copy of this table.

set_columns
(flags, location=None, location_offset=None, metadata=None, metadata_offset=None)¶ Sets the values for each column in this
IndividualTable
using the values in the specified arrays. Overwrites any data currently stored in the table.The
flags
array is mandatory and defines the number of individuals the table will contain. Thelocation
andlocation_offset
parameters must be supplied together, and meet the requirements for Encoding ragged columns. Themetadata
andmetadata_offset
parameters must be supplied together, and meet the requirements for Encoding ragged columns. See Binary columns for more information.Parameters:  flags (numpy.ndarray, dtype=np.uint32) – The bitwise flags for each individual. Required.
 location (numpy.ndarray, dtype=np.float64) – The flattened location array. Must be specified along
with
location_offset
. If not specified or None, an empty location value is stored for each individual.  location_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the
location
array.  metadata (numpy.ndarray, dtype=np.int8) – The flattened metadata array. Must be specified along
with
metadata_offset
. If not specified or None, an empty metadata value is stored for each individual.  metadata_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the
metadata
array.

class
msprime.
NodeTable
¶ A table defining the nodes in a tree sequence. See the definitions for details on the columns in this table and the tree sequence requirements section for the properties needed for a node table to be a part of a valid tree sequence.
Warning: The numpy arrays returned by table attribute accesses are copies of the underlying data. In particular, this means that you cannot edit the values in the columns by updating the attribute arrays.
NOTE: this behaviour may change in future.
Variables:  time (numpy.ndarray, dtype=np.float64) – The array of time values.
 flags (numpy.ndarray, dtype=np.uint32) – The array of flags values.
 population (numpy.ndarray, dtype=np.int32) – The array of population IDs.
 individual (numpy.ndarray, dtype=np.int32) – The array of individual IDs that each node belongs to.
 metadata (numpy.ndarray, dtype=np.int8) – The flattened array of binary metadata values. See Binary columns for more details.
 metadata_offset (numpy.ndarray, dtype=np.uint32) – The array of offsets into the metadata column. See Binary columns for more details.

add_row
(flags=0, time=0, population=1, individual=1, metadata=None)¶ Adds a new row to this
NodeTable
and returns the ID of the corresponding node.Parameters:  flags (int) – The bitwise flags for the new node.
 time (float) – The birth time for the new node.
 population (int) – The ID of the population in which the new node was born.
Defaults to the
NULL_POPULATION
.  individual (int) – The ID of the individual in which the new node was born.
Defaults to the
NULL_INDIVIDUAL
.  metadata (bytes) – The binaryencoded metadata for the new node. If not specified or None, a zerolength byte string is stored.
Returns: The ID of the newly added node.
Return type:

append_columns
(flags, time, population=None, individual=None, metadata=None, metadata_offset=None)¶ Appends the specified arrays to the end of the columns in this
NodeTable
. This allows many new rows to be added at once.The
flags
,time
andpopulation
arrays must all be of the same length, which is equal to the number of nodes that will be added to the table. Themetadata
andmetadata_offset
parameters must be supplied together, and meet the requirements for Encoding ragged columns. See Binary columns for more information.Parameters:  flags (numpy.ndarray, dtype=np.uint32) – The bitwise flags for each node. Required.
 time (numpy.ndarray, dtype=np.float64) – The time values for each node. Required.
 population (numpy.ndarray, dtype=np.int32) – The population values for each node. If not specified
or None, the
NULL_POPULATION
value is stored for each node.  individual (numpy.ndarray, dtype=np.int32) – The individual values for each node. If not specified
or None, the
NULL_INDIVIDUAL
value is stored for each node.  metadata (numpy.ndarray, dtype=np.int8) – The flattened metadata array. Must be specified along
with
metadata_offset
. If not specified or None, an empty metadata value is stored for each node.  metadata_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the
metadata
array.

clear
()¶ Deletes all rows in this table.

copy
()¶ Returns a deep copy of this table.

set_columns
(flags, time, population=None, individual=None, metadata=None, metadata_offset=None)¶ Sets the values for each column in this
NodeTable
using the values in the specified arrays. Overwrites any data currently stored in the table.The
flags
,time
andpopulation
arrays must all be of the same length, which is equal to the number of nodes the table will contain. Themetadata
andmetadata_offset
parameters must be supplied together, and meet the requirements for Encoding ragged columns. See Binary columns for more information.Parameters:  flags (numpy.ndarray, dtype=np.uint32) – The bitwise flags for each node. Required.
 time (numpy.ndarray, dtype=np.float64) – The time values for each node. Required.
 population (numpy.ndarray, dtype=np.int32) – The population values for each node. If not specified
or None, the
NULL_POPULATION
value is stored for each node.  individual (numpy.ndarray, dtype=np.int32) – The individual values for each node. If not specified
or None, the
NULL_INDIVIDUAL
value is stored for each node.  metadata (numpy.ndarray, dtype=np.int8) – The flattened metadata array. Must be specified along
with
metadata_offset
. If not specified or None, an empty metadata value is stored for each node.  metadata_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the
metadata
array.

class
msprime.
EdgeTable
¶ A table defining the edges in a tree sequence. See the definitions for details on the columns in this table and the tree sequence requirements section for the properties needed for an edge table to be a part of a valid tree sequence.
Warning: The numpy arrays returned by table attribute accesses are copies of the underlying data. In particular, this means that you cannot edit the values in the columns by updating the attribute arrays.
NOTE: this behaviour may change in future.
Variables:  left (numpy.ndarray, dtype=np.float64) – The array of left coordinates.
 right (numpy.ndarray, dtype=np.float64) – The array of right coordinates.
 parent (numpy.ndarray, dtype=np.int32) – The array of parent node IDs.
 child (numpy.ndarray, dtype=np.int32) – The array of child node IDs.

add_row
(left, right, parent, child)¶ Adds a new row to this
EdgeTable
and returns the ID of the corresponding edge.Parameters: Returns: The ID of the newly added edge.
Return type:

append_columns
(left, right, parent, child)¶ Appends the specified arrays to the end of the columns of this
EdgeTable
. This allows many new rows to be added at once.All four parameters are mandatory, and must be numpy arrays of the same length (which is equal to the number of additional edges to add to the table).
Parameters:  left (numpy.ndarray, dtype=np.float64) – The left coordinates (inclusive).
 right (numpy.ndarray, dtype=np.float64) – The right coordinates (exclusive).
 parent (numpy.ndarray, dtype=np.int32) – The parent node IDs.
 child (numpy.ndarray, dtype=np.int32) – The child node IDs.

clear
()¶ Deletes all rows in this table.

copy
()¶ Returns a deep copy of this table.

set_columns
(left, right, parent, child)¶ Sets the values for each column in this
EdgeTable
using the values in the specified arrays. Overwrites any data currently stored in the table.All four parameters are mandatory, and must be numpy arrays of the same length (which is equal to the number of edges the table will contain).
Parameters:  left (numpy.ndarray, dtype=np.float64) – The left coordinates (inclusive).
 right (numpy.ndarray, dtype=np.float64) – The right coordinates (exclusive).
 parent (numpy.ndarray, dtype=np.int32) – The parent node IDs.
 child (numpy.ndarray, dtype=np.int32) – The child node IDs.

class
msprime.
MigrationTable
¶ A table defining the migrations in a tree sequence. See the definitions for details on the columns in this table and the tree sequence requirements section for the properties needed for a migration table to be a part of a valid tree sequence.
Warning: The numpy arrays returned by table attribute accesses are copies of the underlying data. In particular, this means that you cannot edit the values in the columns by updating the attribute arrays.
NOTE: this behaviour may change in future.
Variables:  left (numpy.ndarray, dtype=np.float64) – The array of left coordinates.
 right (numpy.ndarray, dtype=np.float64) – The array of right coordinates.
 node (numpy.ndarray, dtype=np.int32) – The array of node IDs.
 source (numpy.ndarray, dtype=np.int32) – The array of source population IDs.
 dest (numpy.ndarray, dtype=np.int32) – The array of destination population IDs.
 time (numpy.ndarray, dtype=np.float64) – The array of time values.

add_row
(left, right, node, source, dest, time)¶ Adds a new row to this
MigrationTable
and returns the ID of the corresponding migration.Parameters: Returns: The ID of the newly added migration.
Return type:

append_columns
(left, right, node, source, dest, time)¶ Appends the specified arrays to the end of the columns of this
MigrationTable
. This allows many new rows to be added at once.All six parameters are mandatory, and must be numpy arrays of the same length (which is equal to the number of additional migrations to add to the table).
Parameters:  left (numpy.ndarray, dtype=np.float64) – The left coordinates (inclusive).
 right (numpy.ndarray, dtype=np.float64) – The right coordinates (exclusive).
 node (numpy.ndarray, dtype=np.int32) – The node IDs.
 source (numpy.ndarray, dtype=np.int32) – The source population IDs.
 dest (numpy.ndarray, dtype=np.int32) – The destination population IDs.
 time (numpy.ndarray, dtype=np.int64) – The time of each migration.

clear
()¶ Deletes all rows in this table.

copy
()¶ Returns a deep copy of this table.

set_columns
(left, right, node, source, dest, time)¶ Sets the values for each column in this
MigrationTable
using the values in the specified arrays. Overwrites any data currently stored in the table.All six parameters are mandatory, and must be numpy arrays of the same length (which is equal to the number of migrations the table will contain).
Parameters:  left (numpy.ndarray, dtype=np.float64) – The left coordinates (inclusive).
 right (numpy.ndarray, dtype=np.float64) – The right coordinates (exclusive).
 node (numpy.ndarray, dtype=np.int32) – The node IDs.
 source (numpy.ndarray, dtype=np.int32) – The source population IDs.
 dest (numpy.ndarray, dtype=np.int32) – The destination population IDs.
 time (numpy.ndarray, dtype=np.int64) – The time of each migration.

class
msprime.
SiteTable
¶ A table defining the sites in a tree sequence. See the definitions for details on the columns in this table and the tree sequence requirements section for the properties needed for a site table to be a part of a valid tree sequence.
Warning: The numpy arrays returned by table attribute accesses are copies of the underlying data. In particular, this means that you cannot edit the values in the columns by updating the attribute arrays.
NOTE: this behaviour may change in future.
Variables:  position (numpy.ndarray, dtype=np.float64) – The array of site position coordinates.
 ancestral_state (numpy.ndarray, dtype=np.int8) – The flattened array of ancestral state strings. See Text columns for more details.
 ancestral_state_offset (numpy.ndarray, dtype=np.uint32) – The offsets of rows in the ancestral_state array. See Text columns for more details.
 metadata (numpy.ndarray, dtype=np.int8) – The flattened array of binary metadata values. See Binary columns for more details.
 metadata_offset (numpy.ndarray, dtype=np.uint32) – The array of offsets into the metadata column. See Binary columns for more details.

add_row
(position, ancestral_state, metadata=None)¶ Adds a new row to this
SiteTable
and returns the ID of the corresponding site.Parameters: Returns: The ID of the newly added site.
Return type:

append_columns
(position, ancestral_state, ancestral_state_offset, metadata=None, metadata_offset=None)¶ Appends the specified arrays to the end of the columns of this
SiteTable
. This allows many new rows to be added at once.The
position
,ancestral_state
andancestral_state_offset
parameters are mandatory, and must be 1D numpy arrays. The length of theposition
array determines the number of additional rows to add the table. Theancestral_state
andancestral_state_offset
parameters must be supplied together, and meet the requirements for Encoding ragged columns (see Text columns for more information). Themetadata
andmetadata_offset
parameters must be supplied together, and meet the requirements for Encoding ragged columns (see Binary columns for more information).Parameters:  position (numpy.ndarray, dtype=np.float64) – The position of each site in genome coordinates.
 ancestral_state (numpy.ndarray, dtype=np.int8) – The flattened ancestral_state array. Required.
 ancestral_state_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the
ancestral_state
array.  metadata (numpy.ndarray, dtype=np.int8) – The flattened metadata array. Must be specified along
with
metadata_offset
. If not specified or None, an empty metadata value is stored for each node.  metadata_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the
metadata
array.

clear
()¶ Deletes all rows in this table.

copy
()¶ Returns a deep copy of this table.

set_columns
(position, ancestral_state, ancestral_state_offset, metadata=None, metadata_offset=None)¶ Sets the values for each column in this
SiteTable
using the values in the specified arrays. Overwrites any data currently stored in the table.The
position
,ancestral_state
andancestral_state_offset
parameters are mandatory, and must be 1D numpy arrays. The length of theposition
array determines the number of rows in table. Theancestral_state
andancestral_state_offset
parameters must be supplied together, and meet the requirements for Encoding ragged columns (see Text columns for more information). Themetadata
andmetadata_offset
parameters must be supplied together, and meet the requirements for Encoding ragged columns (see Binary columns for more information).Parameters:  position (numpy.ndarray, dtype=np.float64) – The position of each site in genome coordinates.
 ancestral_state (numpy.ndarray, dtype=np.int8) – The flattened ancestral_state array. Required.
 ancestral_state_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the
ancestral_state
array.  metadata (numpy.ndarray, dtype=np.int8) – The flattened metadata array. Must be specified along
with
metadata_offset
. If not specified or None, an empty metadata value is stored for each node.  metadata_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the
metadata
array.

class
msprime.
MutationTable
¶ A table defining the mutations in a tree sequence. See the definitions for details on the columns in this table and the tree sequence requirements section for the properties needed for a mutation table to be a part of a valid tree sequence.
Warning: The numpy arrays returned by table attribute accesses are copies of the underlying data. In particular, this means that you cannot edit the values in the columns by updating the attribute arrays.
NOTE: this behaviour may change in future.
Variables:  site (numpy.ndarray, dtype=np.int32) – The array of site IDs.
 node (numpy.ndarray, dtype=np.int32) – The array of node IDs.
 derived_state (numpy.ndarray, dtype=np.int8) – The flattened array of derived state strings. See Text columns for more details.
 derived_state_offset (numpy.ndarray, dtype=np.uint32) – The offsets of rows in the derived_state array. See Text columns for more details.
 parent (numpy.ndarray, dtype=np.int32) – The array of parent mutation IDs.
 metadata (numpy.ndarray, dtype=np.int8) – The flattened array of binary metadata values. See Binary columns for more details.
 metadata_offset (numpy.ndarray, dtype=np.uint32) – The array of offsets into the metadata column. See Binary columns for more details.

add_row
(site, node, derived_state, parent=1, metadata=None)¶ Adds a new row to this
MutationTable
and returns the ID of the corresponding mutation.Parameters:  site (int) – The ID of the site that this mutation occurs at.
 node (int) – The ID of the first node inheriting this mutation.
 derived_state (str) – The state of the site at this mutation’s node.
 parent (int) – The ID of the parent mutation. If not specified,
defaults to the
NULL_MUTATION
.  metadata (bytes) – The binaryencoded metadata for the new node. If not specified or None, a zerolength byte string is stored.
Returns: The ID of the newly added mutation.
Return type:

append_columns
(site, node, derived_state, derived_state_offset, parent=None, metadata=None, metadata_offset=None)¶ Appends the specified arrays to the end of the columns of this
MutationTable
. This allows many new rows to be added at once.The
site
,node
,derived_state
andderived_state_offset
parameters are mandatory, and must be 1D numpy arrays. Thesite
andnode
(alsoparent
, if supplied) arrays must be of equal length, and determine the number of additional rows to add to the table. Thederived_state
andderived_state_offset
parameters must be supplied together, and meet the requirements for Encoding ragged columns (see Text columns for more information). Themetadata
andmetadata_offset
parameters must be supplied together, and meet the requirements for Encoding ragged columns (see Binary columns for more information).Parameters:  site (numpy.ndarray, dtype=np.int32) – The ID of the site each mutation occurs at.
 node (numpy.ndarray, dtype=np.int32) – The ID of the node each mutation is associated with.
 derived_state (numpy.ndarray, dtype=np.int8) – The flattened derived_state array. Required.
 derived_state_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the
derived_state
array.  parent (numpy.ndarray, dtype=np.int32) – The ID of the parent mutation for each mutation.
 metadata (numpy.ndarray, dtype=np.int8) – The flattened metadata array. Must be specified along
with
metadata_offset
. If not specified or None, an empty metadata value is stored for each node.  metadata_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the
metadata
array.

clear
()¶ Deletes all rows in this table.

copy
()¶ Returns a deep copy of this table.

set_columns
(site, node, derived_state, derived_state_offset, parent=None, metadata=None, metadata_offset=None)¶ Sets the values for each column in this
MutationTable
using the values in the specified arrays. Overwrites any data currently stored in the table.The
site
,node
,derived_state
andderived_state_offset
parameters are mandatory, and must be 1D numpy arrays. Thesite
andnode
(alsoparent
, if supplied) arrays must be of equal length, and determine the number of rows in the table. Thederived_state
andderived_state_offset
parameters must be supplied together, and meet the requirements for Encoding ragged columns (see Text columns for more information). Themetadata
andmetadata_offset
parameters must be supplied together, and meet the requirements for Encoding ragged columns (see Binary columns for more information).Parameters:  site (numpy.ndarray, dtype=np.int32) – The ID of the site each mutation occurs at.
 node (numpy.ndarray, dtype=np.int32) – The ID of the node each mutation is associated with.
 derived_state (numpy.ndarray, dtype=np.int8) – The flattened derived_state array. Required.
 derived_state_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the
derived_state
array.  parent (numpy.ndarray, dtype=np.int32) – The ID of the parent mutation for each mutation.
 metadata (numpy.ndarray, dtype=np.int8) – The flattened metadata array. Must be specified along
with
metadata_offset
. If not specified or None, an empty metadata value is stored for each node.  metadata_offset (numpy.ndarray, dtype=np.uint32.) – The offsets into the
metadata
array.

class
msprime.
PopulationTable
¶ A table defining the populations referred to in a tree sequence. The PopulationTable stores metadata for populations that may be referred to in the NodeTable and MigrationTable”. Note that although nodes may be associated with populations, this association is stored in the
NodeTable
: only metadata on each population is stored in the population table.Warning: The numpy arrays returned by table attribute accesses are copies of the underlying data. In particular, this means that you cannot edit the values in the columns by updating the attribute arrays.
NOTE: this behaviour may change in future.
Variables:  metadata (numpy.ndarray, dtype=np.int8) – The flattened array of binary metadata values. See Binary columns for more details.
 metadata_offset (numpy.ndarray, dtype=np.uint32) – The array of offsets into the metadata column. See Binary columns for more details.

add_row
(metadata=None)¶ Adds a new row to this
PopulationTable
and returns the ID of the corresponding population.Parameters: metadata (bytes) – The binaryencoded metadata for the new population. If not specified or None, a zerolength byte string is stored. Returns: The ID of the newly added population. Return type: int

clear
()¶ Deletes all rows in this table.

copy
()¶ Returns a deep copy of this table.

class
msprime.
ProvenanceTable
¶ A table recording the provenance (i.e., history) of this table, so that the origin of the underlying data and sequence of subsequent operations can be traced. Each row contains a “record” string (recommended format: JSON) and a timestamp.
Todo
The format of the record field will be more precisely specified in the future.
Variables:  record (numpy.ndarray, dtype=np.int8) – The flattened array containing the record strings. Text columns for more details.
 record_offset (numpy.ndarray, dtype=np.uint32) – The array of offsets into the record column. See Text columns for more details.
 timestamp (numpy.ndarray, dtype=np.int8) – The flattened array containing the timestamp strings. Text columns for more details.
 timestamp_offset (numpy.ndarray, dtype=np.uint32) – The array of offsets into the timestamp column. See Text columns for more details.

add_row
(record, timestamp=None)¶ Adds a new row to this ProvenanceTable consisting of the specified record and timestamp. If timestamp is not specified, it is automatically generated from the current time.
Parameters:

clear
()¶ Deletes all rows in this table.

copy
()¶ Returns a deep copy of this table.
Table Collections¶
Each of the table classes defines a different aspect of the structure of
a tree sequence. It is convenient to be able to refer to a set of these
tables which together define a tree sequence. We
refer to this grouping of related tables as a TableCollection
.
The TableCollection
and TreeSequence
classes are
deeply related. A TreeSequence
instance is based on the information
encoded in a TableCollection
. Tree sequences are immutable, and
provide methods for obtaining trees from the sequence. A TableCollection
is mutable, and does not have any methods for obtaining trees.
The TableCollection
class essentially exists to allow the
dynamic creation of tree sequences.

class
msprime.
TableCollection
(sequence_length=0)¶ A collection of mutable tables defining a tree sequence. See the Data model section for definition on the various tables and how they together define a
TreeSequence
. Arbitrary data can be stored in a TableCollection, but there are certain requirements that must be satisfied for these tables to be interpreted as a tree sequence.To obtain a
TreeSequence
instance corresponding to the current state of aTableCollection
, please use thetree_sequence()
method.Variables:  individuals (IndividualTable) – The individual table.
 nodes (NodeTable) – The node table.
 edges (EdgeTable) – The edge table.
 migrations (MigrationTable) – The migration table.
 sites (SiteTable) – The site table.
 mutations (MutationTable) – The mutation table.
 populations (PopulationTable) – The population table.
 provenances (ProvenanceTable) – The provenance table.
 sequence_length (float) – The sequence length defining the coordinate space.

asdict
()¶ Returns this TableCollection as a dictionary mapping the keys “nodes”, “edges”, etc to their respective table objects.

compute_mutation_parents
()¶ Modifies the tables in place, computing the
parent
column of the mutation table. For this to work, the node and edge tables must be valid, and the site and mutation tables must be sorted (seeTableCollection.sort()
). This will produce an error if mutations are not sorted (i.e., if a mutation appears before its mutation parent) unless the two mutations occur on the same branch, in which case there is no way to detect the error.The
parent
of a given mutation is the ID of the next mutation encountered traversing the tree upwards from that mutation, orNULL_MUTATION
if there is no such mutation.

deduplicate_sites
()¶ Modifies the tables in place, removing entries in the site table with duplicate
position
(and keeping only the first entry for each site), and renumbering thesite
column of the mutation table appropriately. This requires the site table to be sorted by position.

simplify
(samples, filter_zero_mutation_sites=True)¶ Simplifies the tables in place to retain only the information necessary to reconstruct the tree sequence describing the given
samples
. This will change the ID of the nodes, so that the nodesamples[k]
will have IDk
in the result. The resulting NodeTable will have only the firstlen(samples)
individuals marked as samples. The mapping from node IDs in the current set of tables to their equivalent values in the simplified tables is also returned as a numpy array. If an arraya
is returned by this function andu
is the ID of a node in the input table, thena[u]
is the ID of this node in the output table. For any nodeu
that is not mapped into the output tables, this mapping will equal1
.Tables operated on by this function must: be sorted (see
TableCollection.sort()
)), have children be born strictly after their parents, and the intervals on which any individual is a child must be disjoint. Other than this the tables need not satisfy remaining requirements to specify a valid tree sequence (but the resulting tables will).Parameters: Returns: A numpy array mapping node IDs in the input tables to their corresponding node IDs in the output tables.
Return type: numpy array (dtype=np.int32)

sort
(edge_start=0)¶ Sorts the tables in place. This ensures that all tree sequence ordering requirements listed in the Valid tree sequence requirements section are met, as long as each site has at most one mutation (see below).
If the
edge_start
parameter is provided, this specifies the index in the edge table where sorting should start. Only rows with index greater than or equal toedge_start
are sorted; rows before this index are not affected. This parameter is provided to allow for efficient sorting when the user knows that the edges up to a given index are already sorted.The individual, node, population and provenance tables are not affected by this method.
Edges are sorted as follows:
 time of parent, then
 parent node ID, then
 child node ID, then
 left endpoint.
Note that this sorting order exceeds the edge sorting requirements for a valid tree sequence. For a valid tree sequence, we require that all edges for a given parent ID are adjacent, but we do not require that they be listed in sorted order.
Sites are sorted by position, and sites with the same position retain their relative ordering.
Mutations are sorted by site ID, and mutations with the same site retain their relative ordering. This does not currently rearrange tables so that mutations occur after their mutation parents, which is a requirement for valid tree sequences.
Parameters: edge_start (int) – The index in the edge table where sorting starts (default=0; must be <= len(edges)).

tree_sequence
()¶ Returns a
TreeSequence
instance with the structure defined by the tables in thisTableCollection
. If the table collection is not in canonical form (i.e., does not meet sorting requirements) or cannot be interpreted as a tree sequence an exception is raised. Thesort()
method may be used to ensure that input sorting requirements are met.Returns: A TreeSequence
instance reflecting the structures defined in this set of tables.Return type: TreeSequence
Table functions¶

msprime.
parse_nodes
(source, strict=True, encoding='utf8', base64_metadata=True, table=None)¶ Parse the specified filelike object containing a whitespace delimited description of a node table and returns the corresponding
NodeTable
instance. See the node text format section for the details of the required format and the node table definition section for the required properties of the contents.See
load_text()
for a detailed explanation of thestrict
parameter.Parameters:  source (stream) – The filelike object containing the text.
 strict (bool) – If True, require strict tab delimiting (default). If False, a relaxed whitespace splitting algorithm is used.
 encoding (string) – Encoding used for text representation.
 base64_metadata (bool) – If True, metadata is encoded using Base64 encoding; otherwise, as plain text.
 table (NodeTable) – If specified write into this table. If not,
create a new
NodeTable
instance.

msprime.
parse_edges
(source, strict=True, table=None)¶ Parse the specified filelike object containing a whitespace delimited description of a edge table and returns the corresponding
EdgeTable
instance. See the edge text format section for the details of the required format and the edge table definition section for the required properties of the contents.See
load_text()
for a detailed explanation of thestrict
parameter.Parameters:  source (stream) – The filelike object containing the text.
 strict (bool) – If True, require strict tab delimiting (default). If False, a relaxed whitespace splitting algorithm is used.
 table (EdgeTable) – If specified, write the edges into this table. If
not, create a new
EdgeTable
instance and return.

msprime.
parse_sites
(source, strict=True, encoding='utf8', base64_metadata=True, table=None)¶ Parse the specified filelike object containing a whitespace delimited description of a site table and returns the corresponding
SiteTable
instance. See the site text format section for the details of the required format and the site table definition section for the required properties of the contents.See
load_text()
for a detailed explanation of thestrict
parameter.Parameters:  source (stream) – The filelike object containing the text.
 strict (bool) – If True, require strict tab delimiting (default). If False, a relaxed whitespace splitting algorithm is used.
 encoding (string) – Encoding used for text representation.
 base64_metadata (bool) – If True, metadata is encoded using Base64 encoding; otherwise, as plain text.
 table (SiteTable) – If specified write site into this table. If not,
create a new
SiteTable
instance.

msprime.
parse_mutations
(source, strict=True, encoding='utf8', base64_metadata=True, table=None)¶ Parse the specified filelike object containing a whitespace delimited description of a mutation table and returns the corresponding
MutationTable
instance. See the mutation text format section for the details of the required format and the mutation table definition section for the required properties of the contents.See
load_text()
for a detailed explanation of thestrict
parameter.Parameters:  source (stream) – The filelike object containing the text.
 strict (bool) – If True, require strict tab delimiting (default). If False, a relaxed whitespace splitting algorithm is used.
 encoding (string) – Encoding used for text representation.
 base64_metadata (bool) – If True, metadata is encoded using Base64 encoding; otherwise, as plain text.
 table (MutationTable) – If specified, write mutations into this table.
If not, create a new
MutationTable
instance.

msprime.
pack_strings
(strings, encoding='utf8')¶ Packs the specified list of strings into a flattened numpy array of 8 bit integers and corresponding offsets using the specified text encoding. See Encoding ragged columns for details of this encoding of columns of variable length data.
Parameters: Returns: The tuple (packed, offset) of numpy arrays representing the flattened input data and offsets.
Return type: numpy.array (dtype=np.int8), numpy.array (dtype=np.uint32)

msprime.
unpack_strings
(packed, offset, encoding='utf8')¶ Unpacks a list of strings from the specified numpy arrays of packed byte data and corresponding offsets using the specified text encoding. See Encoding ragged columns for details of this encoding of columns of variable length data.
Parameters:  packed (numpy.ndarray) – The flattened array of byte values.
 offset (numpy.ndarray) – The array of offsets into the
packed
array.  encoding (str) – The text encoding to use when converting string data
to bytes. See the
codecs
module for information on available string encodings.
Returns: The list of strings unpacked from the parameter arrays.
Return type:

msprime.
pack_bytes
(data)¶ Packs the specified list of bytes into a flattened numpy array of 8 bit integers and corresponding offsets. See Encoding ragged columns for details of this encoding.
Parameters: data (list[bytes]) – The list of bytes values to encode. Returns: The tuple (packed, offset) of numpy arrays representing the flattened input data and offsets. Return type: numpy.array (dtype=np.int8), numpy.array (dtype=np.uint32)

msprime.
unpack_bytes
(packed, offset)¶ Unpacks a list of bytes from the specified numpy arrays of packed byte data and corresponding offsets. See Encoding ragged columns for details of this encoding.
Parameters:  packed (numpy.ndarray) – The flattened array of byte values.
 offset (numpy.ndarray) – The array of offsets into the
packed
array.
Returns: The list of bytes values unpacked from the parameter arrays.
Return type: