Hmmalign aligns sequences to a profile HMM. Make a multiple alignment of many sequences to a common profile HMM. Perform a multiple sequence alignment of all the sequences in
Parent program: hmmer
HMMER software allows search for protein homologs and also permits multiple protein sequence alignment. Unlike BLAST, HMMER uses probabilistic models called profile hidden Markov models which provide a significantly more accurate and more sensitive detection of remote homologs. The HMMER software suite has been widely used, particularly for protein family databases such as Pfam and InterPro and their associated search tools. Also HMMER has several programs for protein sequence analysis such as phmmer, hmmscan, hmmsearch and jackhmmer.