UIcluster is an updated version of tlcluster that is much faster and adds new features such as reverse complement checking. In addition to optimization and reverse checking, it performs an extended search of all primaries for each sequence being clustered.
genBlast is a program suite, consisting of two programs: genBlastA and genBlastG.
genBlastA parses local alignments, or high-scoring segment pairs (HSPs) produced by local sequence alignment programs such as BLAST and WU-BLAST and identify groups of HSPs. Each HSP group represent a putative gene that is homologous to the query protein (gene).
genBlastG is a fast homology-based gene finder. It builds on genBlastA. In particular, it takes genBlastA output as input and define gene models baesd on the HSP group.