A pipline to test for homogeneity in large datasets
To run this script you need Python 3 and the following dependencies: Biopython, math, itertools, numpy, pandas, shutil, glob, random, and linecache.
First you should define the clades in a text file as follows:
- If you have n taxa that you want to group in k clades then your text file should include k lines that represents the different clades.
Each line have the names of the taxa in that clade, separated by a coma.You can find an example in
clades.txt - Run
Extract_clades_alignmet.pyas follow:
Extract_clades_alignments.py <alignment_file> <alignment_fromat> <clades_file> <clades_dir>
<alignment_file> The full alignment with all taxa
<alignment_fromat> The format of the alignment. possible formats: fasta, phylip, or nexus
<clades_file> text file that where each line represents a clade. Taxa in each clade/line are separated by a coma. e.g.clades.txt
Note: make sure that the taxa names are the same as they appear in the alignment file.
<clades_dir> Directory where you want to save all the clades' alignments