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Protpipeliner

This script combines MUSCLE, GBLOCKS, Prottest and RaxML for an efficient and streamlined method of building trees.

IMPORTANT alternative script

protpipeliner-pplacer.py

This version limits model selection to those compatible with pplacer.

Example usage: protpipeliner.py -i dmso_fortree_aligned.fasta -t 10 -b 100 -m low -a T

Example further stepd for creating a DRAM2 .refpkg for Trees:

  1. Determine the number of positions:
seqkit stats dmso_refs.fasta.al
#Output:
#file                format  type     num_seqs  sum_len  min_len  avg_len  max_len
#dmso_refs.fasta.al  FASTA   Protein        86  160,046    1,861    1,861    1,861
  1. Create the .refpkg
taxit create -P dmso_package -l 1861 -p dmso_refs.fasta.model -f RAxML_info.dmso_refs.fasta --stats-type RAxML

The main protpipeliner.py script does not rename the alignment file. Use rename-alignment.py to rename this. This is needed for DRAM2 trees .refpkg:

Example usage:

python rename-alignment.py dmso_refs.fasta dmso_refs.fasta.al renamed_dmso_alignment.al