get_coalescent_codon.py Coalescent-based tree estimated from concatenated alignments of single gene first codon and second codon positions, third codon positions.
get_concatenated_codon.py Concatenated-based tree estimated from concatenated alignments of all genes of first and second codon positions, third codon positions
get_strictly_single_copy_orthogroup.py This script is for select strictly single copy orthogroup form OrthoMCL
get_mostly_single_copy_orthogroup.py This script is for select mostly single copy orthogroup from OrthoMCL
get_supermatrix_from_MSA_for_low_copy.py This script is for get concatenated-based alignments (supermatrix) from OrthoMCL