selectClassSite

selectClassSite is program to extract sites from a alignment of coding sequence in fasta or phylip format. This program is written using the Bio ++ library (Guéguen et al. 2013).

You can use the static executable compiled for linux x64 computer (see Release). You can also compile the program assuming that you have Bio ++ installed (here the Bio++ library V2 is locally installed in $HOME/local/bpp/dev/ directory).

Please cite Bio++ if you use this program:

• Guéguen L, Gaillard S, Boussau B, Gouy M, Groussin M, Rochette NC, Bigot T, Fournier D, Pouyet F, Cahais V, et al. 2013. Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution. Mol. Biol. Evol. 30:1745–1750.

Author: Benoit Nabholz

Option

selectClassSite file_name fomat 'Standard or VertebrateMitochondrial or InvertebrateMitochondrial' 'L4 or third or independent_codon'

• format : fasta or phylip
• third: Extract third codon position
• L4: Extract fourfold degenerate site
• independent_codon: print two files with independent codon (selected randomly)

Example of usage to extract the 4-fold denerate site from a alignment (align.fata)

selectClassSite align.fasta fasta Standard L4