idwtree

Protein BLAST analysis finds all homologs of a protein; however, for many
analyses, it is important to identify orthologs in different species (e.g. homologs
that derive from the same ancestral sequence). The program idwtree aid in this
analysis by assigning 'group' identity in phylogenetic trees containing
reference sequences as markers.

The standard workflow idwtree was intended to analyze:
1. BLAST protein sequence of interest against organism(s) of interest.
2. Download all significant BLAST hits.
3. Build a multiple sequence alignment of BLAST hits with reference sequences (e.g.
with CLUSTAL OMEGA or MAFFT).
4. Use the alignment to build a phylogenetic tree (e.g. with the PHYLIP package)
5. Use idwtree to assign BLAST hits to ortholog groups