HMMER is a widely used sequence search software similar to BLAST, used specially for searching DNA and protein databases for homologs
The stronger point of HMMER is that it takes the alignment of a couple of sequences as a input and constructs a position-specific-scoring-matrix (PSSM) based profil of the input alignment (or query sequence). These profiles are actually probabilistic profile hidden markov models.
The profile is then further used to search the databases and create alignments.
Other similar software are SAM Tools, PSI-BLAST.
HMMER suite actually contains a number of small standalone program that are used to implement he entire functionality.
A quick read tutorial can be found here.