There is an treeing algorithm, originated by Geert De Soete,
that seems to be known for its speed (I don't use it myself).
It is available as C source in the GDE version 1.0 sequence
editor package (you also need a companion program "count"
to convert sequences to a distance matrix which the DeSoete
"lsadt" program uses). This program is distributed thru
the Ribosomal Database Project, where it is also used in
treeing the ribosome data.
Here is an ftp reference:
Here are some details of the method:
This program uses a least squares fitting method to determine
additive trees from a given distance matrix. The tree generated
is passed back in Newick format. The prefered method of displaying
the phylogenetic results is in TreeTool.
LEAST SQUARES ALGORITHM FOR FITTING ADDITIVE TREES TO
GEERT DE SOETE -- VERSION 1.01 - FEB. 1983
VERSION 1.02 - JUNE 1983
VERSION 1.03 - JULY 1983
'C' version by Michael Macuikenas, University of Illinois
REFERENCE: DE SOETE, G. A LEAST SQUARES ALGORITHM FOR FITTING
ADDITIVE TREES TO PROXIMITY DATA. PSYCHOMETRIKA, 1983, 48,
DE SOETE, G. ADDITIVE TREE REPRESENTATIONS OF INCOMPLETE
DISSIMILARITY DATA. QUALITY AND QUANTITY, 1984, 18,
Don Gilbert gilbert at bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405