NJTree Phyml
From BioPerl
NJTREE is a tree building program primarily in use in the TreeFam and EnsEMBL Compara databases. It is able to reconstruct trees by means of neighbor-joining (NJ) or extended maximum-likelihood (ML), inferring duplications/losses as well as orthologs/paralogs.
NJTREE is particularly useful in the reconstruction of a gene tree for a gene family with know species phylogenies.
