Protein sequence alignment

Protein sequence alignment tools include

For finding distant homologs

• Smith-Waterman
• FASTA with an appropriate substitution matrix (BLOSUM45, BLOSUM50, BLOSUM62)
• BLASTP with an appropriate substitution matrix (BLOSUM45, BLOSUM50, BLOSUM62)

For finding homologs based on an alignment

• PSI-BLAST
• HMMER
• FASTA can also be run with the profile generated from PSI-BLAST

For finding exact or nearly exact matches quickly

• PMATCH
• BLAT
• SSAHA
• BLASTP with a high stringency and matrix like BLOSUM90 or PAM30.