gb2genes.pl ; Extract Genes from GenBank to FASTA

mol2paml.pl ; Convert MOLPHY format to PAML format which is also compatible with MOLPHY and PHYLIP

mol2T3.pl ; Convert MOLPHY/PAML sequencial format file to T3 (estbranches) format

lnf2lls.pl ; Convert lnf (PAML output file) to lls (input file for totalml of MOLPHY)

picklnf.pl ; Pickup lnf data for particular tree(s) listed in a file

joinlnf.pl ; Join lnf data calculated with segmented tree pool for economy of computing time with PAML

catvt.pl ; Display log likelihood values of consel result

consel2consens.pl ; Convert consel (catpv) output file to PHYLIP (consens) infile for calculation of consensus

ami2a_m_i_fas.pl ; Beautify AA sequences in FASTA format to align with nucleotides

fakeread.pl ; Make trace and phred files from a FASTA file and move to chromat_dir and phd_dir

ref2fakeread.pl ; Make FASTA, trace and phred files from a PHD file and move to chromat_dir and phd_dir (Make a reference seq from an existing read)

pickfas.pl ; Pickup FASTA sequences designated in a list file from a multi-fasta file.

consed.bat (csh script) ; Call bases, assemble and run consed on many projects assemblies one after another