This script parses the log file from phyluce_assembly_match_contigs_to_probes to more easily output locus, contig etc. counts.
python match_contigs_log_parse.py [-h] Infile (Outfile)
Where 'Infile' is the logfile produced by phyluce_assembly_match_contigs_to_probes.
This script searches a directory of Garli best tree files, and finds the one with the maximum likelihood.
Run from directory with tree files.
Wrapper shell script for automating the entire Phyluce pipeline into one command.
Script tells you what you need to run it, but a working knowledge of how to run Phyluce is helpful.
I've tested a version of this script on a cluster, but never a local machine. Should work though. If you try it and their are problems, let me know. If you are interested in adapting the cluster version to your particular cluster, let me know and I can send you that version too.
Wrapper shell script for automating the Phyluce pipeline following the match_contigs_to_probes step into one command. Gives the ability to run different 'taxon-groups' without having to digest the entire script.
Script tells you what you need to run it, but a working knowledge of how to run Phyluce is helpful.
I've tested a version of this script on a cluster, but never a local machine. Should work though. If you try it and there are problems, let me know. If you are interested in adapting the cluster version to your particular cluster, let me know and I can send you that version too.