aa_recoder.py

Recode an input matrix based on various amino acid classification strategies.

aa_recoder.py [OPTIONS] -i <input_matrix> -re <input_strategy>

Required arguments:

• -i, --input <matrix.fas|nex|phy> Path to input matrix
• -re, --recoding_strat <strategy> Desired amino acid recoding strategy
  • Options: SR4, SR6, KGB6, D6, D9, D12, D15, D18

Optional arguments:

• --in_format <format> Input file format if not fasta
  • Options: fasta, phylip (names truncated at 10 characters), phylip-relaxed (names are not truncated), or nexus
  • Default: fasta
• -o, --output <out_dir> Path to user-defined output directory
  • Default: ./aa_recoder_out_<M.D.Y>
• -h, --help Show this help message and exit

Default aa_recoder.py output:

• the input matrix in fasta format with amino acids re-coded to on your chosen amino acid binning strategy. Options include SR4, SR6, KGB6, Dayhoff6, Dayhoff9, Dayhoff12, Dayhoff15, and Dayhoff18. Recoding strategies follow methods outlined in Dayhoff et al. 1978, Susko and Rogers 2007, Kosiol et al. 2004, Feuda et al. 2017, and Hernandez and Ryan 2021.