Programs used in the lab for various tasks
getRBH.pl program for obtaining reciprocal best hits (RBH) using either of blastp, mmseqs, diamond, or lastal
calcANI.pl program for obtaining average nucleotide identity (ANI) by several methods.
getdNdS.pl program to obtain non-synonymous to synonymous substitutions with codeml (paml)
scanFams.pl program for runnign domain scans using different programs. These assume you already have the domain databases built
cleanFams.pl this programs takes the output of scanFams.pl and cleans it by eliminating overlapped matches, or matches covering less than some minimal proportion of the domain model