How to run multiple alignment of WGS data in .gb and .fasta formats using Python or Ruby/Java? Please advise some packages and tutorials. I could not find a tutorial on multiple alignment and SNP calling using Python and Ruby. All I could do is to use trial DNAStar, RidomSeqSphere and NextGene software. Are there any free similar software and a way to do it with a modern language? Thank you, Folks.