orthocounts2bin

A script that creates a binary gene presence/absence alignment from Orthogroups.GeneCounts.tsv
This aligment can be used to construct phylogenies based on gene content.

Arguments

Argument	Description
-i filename	file w/ gene counts (from OrthoFinder output)
-o filename	directory to write the output file(s)
-incl filename	file w/ species. Analyze these species only
-excl filename	file w/ species. Remove these species from analysis
-tsv	creates tsv file
-phylip	creates PHYLIP alignment file
-fasta	creates FASTA alignment file

Example usage

python orthocounts2bin.py -i /Users/pnatsi/orthology/Orthogroups.GeneCounts.tsv -o /Users/pnatsi/orthology/ -tsv -fasta

Careful! Only full paths to the input files are currently supported

Who
Paschalis Natsidis, PhD candidate (p.natsidis@ucl.ac.uk);

Where
Telford Lab, UCL;
ITN IGNITE;

When
May 2019;