phylogenetics.py parses and evaluates Blast results for phylogenetic analyses. Run it with -h or --help for more information.
To begin, run phylogenetics.py --init to initialise the folder structure. Create one fasta file in fastas/ for each sequence you want to have analysed. I suggest to run blast on some server (e.g. Stallo). Update nr to the latest version and run blast with the following script (adjust accordingly for multiple files):
$db=/path/to/database
$fn=/path/to/query_filename.fasta
$threads=16 # probably adjust this value depending on the server
blastp -db $db -query $fn -out ${fn%.fasta}.xml -outfmt 5 -max_target_seqs 20000 -evalue 1 -num_threads $threadsMove the resulting xml files to the folder blastresults/.
Run phylogenetics.py --all and examine the results. Especially proteinlist.txt must be changed according to your proteins.
phylotree.py visualizes phylogenetic trees in Newick format. Run it with -h or --help for more information.