Cookbook

Concatenating multiple alignments NEXUS files with the Bio.Nexus module.

The Problem

It is common to make species-level phylogenetic inferences from multiple genes or proteins. Demographic (and other) processes can cause single gene trees to diverge from the species tree, so support from multiple genes for the same tree topology is considered stronger evidence than single gene inferences (of course, we still need to test that each gene is telling the same story).

This is usually handled by aligning each gene separately then creating a single “supermatrix” from the individual gene alignments, i.e. you create a single alignment containing one row for each taxon where the data for each row is the concatenated aligned gene sequences for the taxon. In NEXUS files (used by the phylogenetic software PAUP*, MrBayes, and others) multiple genes can be explicitly represented as different ‘character partitions’ or ‘sets’ within a data matrix that contains one long sequence for each taxon. In this way you can create a supermatrix but still apply different substitution models to each gene within in it or run PAUP*’s Partition Homogeneity Test to check for significant difference in the rate/topology of each gene tree.

The Bio.Nexus module makes concatenating multiple alignments into a supermatrix relatively straight forward.

The Solution

Say we have NEXUS files for three genes, btCOI.nex, btCOII.nex and btITS.nex, containing alignments:

#COI
bt1 GGGGGGGGGGGG
bt2 GGGGGGGGGGGG
bt3 GGGGGGGGGGGG
#COII
bt1 AAAAAAAAAAAA
bt2 AAAAAAAAAAAA
bt3 AAAAAAAAAAAA
#ITS
bt1 -TTTTTTT
bt2 -TTTTTTT
bt3 -TTTTTTT
bt4 -TTTTTTT

We can use the Nexus module to make a supermatrix:

from Bio.Nexus import Nexus

# the combine function takes a list of tuples [(name, nexus instance)...],
# if we provide the file names in a list we can use a list comprehension to
# create these tuples

file_list = ["btCOI.nex", "btCOII.nex", "btITS.nex"]
nexi = [(fname, Nexus.Nexus(fname)) for fname in file_list]

combined = Nexus.combine(nexi)
combined.write_nexus_data(filename=open("btCOMBINED.nex", "w"))

That was easy! Let’s look at our combined file

#NEXUS
begin data;
    dimensions ntax=4 nchar=32;
    format datatype=dna missing=? gap=-;
matrix
bt1 GGGGGGGGGGGG-TTTTTTTAAAAAAAAAAAA
bt2 GGGGGGGGGGGG-TTTTTTTAAAAAAAAAAAA
bt3 GGGGGGGGGGGG-TTTTTTTAAAAAAAAAAAA
bt4 ????????????-TTTTTTT????????????
;
end;

begin sets;
charset btITS.nex = 13-20;
charset btCOI.nex = 1-12;
charset btCOII.nex = 21-32;
charpartition combined = btCOI.nex: 1-12, btITS.nex: 13-20, btCOII.nex: 21-32;
end;

Ahh, it was too easy. The matrices have been combined and the character sets and partitions set up but the ITS file had a taxon (bt4) that wasn’t in the other files. In these cases the combine function adds the taxon with missing data (the ‘?’s) for the other character partitions. Sometimes this might be the result you want but having a few taxa like this is also a very good way to make a Partition Homogeneity Test run for a week. Let’s write a function that tests that the same taxa are represented in a set of nexus instances and provides a useful error message if not (i.e. what to delete from your NEXUS files if you want them to combine nicely).

def check_taxa(matrices):
    """Verify Nexus instances have the same taxa information.

    Checks that nexus instances in a list [(name, instance)...] have
    the same taxa, provides useful error if not and returns None if
    everything matches
    """
    first_taxa = matrices[0][1].taxlabels
    for name, matrix in matrices[1:]:
        first_only = [t for t in first_taxa if t not in matrix.taxlabels]
        new_only = [t for t in matrix.taxlabels if t not in first_taxa]
        if first_only:
            missing = ", ".join(first_only)
            msg = "%s taxa %s not in martix %s" % (nexi[0][0], missing, name)
            raise Nexus.NexusError(msg)
        elif new_only:
            missing = ", ".join(new_only)
            msg = "%s taxa %s not in all matrices" % (name, missing)
            raise Nexus.NexusError(msg)
    return None  # will only get here if it hasn't thrown an exception


def concat(file_list, same_taxa=True):
    """Combine multiple nexus data matrices in one partitioned file.

    By default this will only work if the same taxa are present in each file
    use same_taxa=False if you are not concerned by this
    """
    nexi = [(fname, Nexus.Nexus(fname)) for fname in file_list]
    if same_taxa:
        if not check_taxa(nexi):
            return Nexus.combine(nexi)
    else:
        return Nexus.combine(nexi)

And now, using our new functions:

>>> handles = [open('btCOI.nex', 'r'), open('btCOII.nex', 'r'), open('btITS.nex', 'r')]
# If we combine them all we should get an error and the taxon/taxa that caused it
>>> concat(handles)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "<stdin>", line 5, in concat
  File "<stdin>", line 16, in check_taxa
Bio.Nexus.Nexus.NexusError: btITS.nex taxa bt4 not in all matrices

# But if we use just the first two, which do have matching taxa, it should be fine
>>> concat(handles[:2]).taxlabels
['bt1', 'bt2', 'bt3']

# Ok, can we still munge them together if we want to?
>>> concat(handle, same_taxa=False).taxlabels
['bt1', 'bt2', 'bt3', 'bt4']

Discussion

The details of the Nexus class are provided in the API Documentation.