EMBOSS

EMBOSS is a suite of programs. Here’s a list

Examples

Calculate the percent identity for sequences in an alignment

infoalign dna.align.fasta -only -name -idcount -alignlength -outfile dna.infoalign -heading true

The infoalign output file will then contain entries like

Name        AlignLen    Ident   
Bifidobacterium-adolescentis.NC_008618  321 127
Bifidobacterium-breve.NC_017218 255 106
M39           321   230
R37           321   248
R38           321   248

Generate a consensus sequence for a multiple sequence alignment

cons -sequence dna.align.fasta -outseq dna.consensus.fasta