Basic Local Alignment Search Tool (BLAST) finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
Clustal is a series of widely used computer programs used in Bioinformatics for multiple sequence alignment. We provide ClustalO and ClustalW.