evolver Module

The module will evolve sequences along a phylogeny.

class evolver.Site

Defines the Site class, which holds information for each evolved site.

class evolver.Evolver(**kwargs)

Bases: object

This callable class evolves sequences along a phylogeny. By default, Evolver will evolve sequences and create several output files:

1. simulated_alignment.fasta

   • The resulting simulated alignment

2. site_rates.txt

   • File providing rate information about each simulated column. Gives the partition and rate cateogy for each site in final simulated alignment.
   • Tab-delimited file with fields, Site_Index Partition_Index Rate_Category . All indexing is from 1.

3. site_rates_info.txt

   • File providing the true site-rate heterogeneity values (either the rate scaling factor or dN and dS) for each rate category.
   • Tab-delimited file with fields, Partition_Index Model_Name Rate_Category Rate_Probability Rate_Factor

Note that file creation may be suppressed or files may be renamed using optional arguments given below.

Required keyword arguments include,

1. tree is the phylogeny (parsed with the newick.read_tree function) along which sequences are evolved
2. partitions (or partition) is a list of Partition instances to evolve.

__call__(**kwargs)

Simulate sequences, perform any necessary post-processing, and save sequences and/or other info to appropriate files.

Optional keyword arguments:

1. seqfile is a custom name for the output simulated alignment. Provide None or False to suppress file creation.
2. seqfmt is the format for seqfile (either fasta, nexus, phylip, phylip-relaxed, stockholm, etc. Anything that Biopython can accept!!) Default is FASTA.
3. ratefile is a custom name for the “site_rates.txt” file. Provide None or False to suppress file creation.
4. infofile is a custom name for the “site_rates_info.txt” file. Provide None or False to suppress file creation.
5. write_anc is a boolean argument (True or False) for whether ancestral sequences should be output along with the tip sequences. Default is False.

Examples:

>>> # Set up Evolver instance, and use below in various ways
evolve = Evolver(tree = my_tree, partitions = my_partition_list)

>>> # Evolve according to default settings
>>> evolve()

>>> # Include ancestral sequences in output file
>>> evolve(write_anc = True)

>>> # Custom sequence file name and format, and suppress rate information
>>> evolve(seqfile = "my_seqs.phy", seqfmt = "phylip", ratefile = None, infofile = None)

get_sequences(anc=False)

Method to return the dictionary of simulated sequences. Default anc = False will return the leaf_sites dictionary. If anc == True, then will return the evolved_sites dictionary.