Model Estimation
A script to estimate an amino acid substitution model from a set of alignments using the QMaker program (https://www.biorxiv.org/content/10.1101/2020.02.20.958819v1).

Notes: The script requires the IQ-TREE package (http://www.iqtree.org/). You have to declare the path to your installed IQ-TREE folder at line 34th of the script.

Commands:

python Est.py -d [alignment_directory] -t [number_of_thread] -mset [set_of_models]

Where
-d      The path to a directory containing all training alignments in Phylip format (required).
-t       The number of threads (optional – defaut = 1).
-mset  A set of amino acid substitution models used to select the best-fit models for alignments (optional, default: FLU,
      HIVb, HIVw, JTT, WAG, LG). The models are separated by ‘,’.

Example: python Est.py -d Example

The estimated substitution models will be written to the file [alignment_directory].PAML. The file contains an exchangeability matrix and a frequency vector.