SEQFIRE

SeqFIRE is a program for extracting regions of interest from a multiple sequence alignment. The program can search for and extract region that contain insertions and deletions (indel), and output details of the indel, as well as binary character matrix of conserved simple indels for use in phylogenetic analysis. SeqFIRE can also extract blocks of conserved columns from a sequence alignment, and output these alignments in proper format for phylogenetic analysis.