README
REQUIREMENTS
Python (including BioPython)
Perl (for the MOCATFetchMGs03.pl script for the extraction of the 40 universal single copy marker genes)
usearch (version 6.0 or higher; executable as "usearch")
glsearch (version 36 or higher; executable as "glsearch36")
INSTALLATION
1. download files
2. extract specI_v1.0.tar.gz
3. set binFolder in specI.py script to the extracted "specI_v1.0" folder
USAGE:
Usage: specI.py infileGenes infileProteins threads runName basefolder
infileGenes: fasta file with gene sequences of a genomes
infileProteins: fasta file with protein sequences of a genomes (same gene names as used in infileGenes)
threads: number of threads to be used
runName: name of current run
basefolder: basefolder of current run (a subfolder for each run will be generated automatically)