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MOLPHY: A Computer Program Package for Molecular Phylogenetics
This is the MOLPHY (ProtML) distribution, version 2.3.
Copyright (c) 1992-1996, Jun Adachi & Masami Hasegawa.
All rights reserved.
MOLPHY is a program package for MOLecular PHYlogenetics.
ProtML is a main program in MOLPHY for inferring evolutionary trees from PROTein (amino acid) sequences by using the Maximum Likelihood method.

Programs (C language)

ProtML: Maximum Likelihood Inference of Protein Phylogeny
NucML: Maximum Likelihood Inference of Nucleic Acid Phylogeny
ProtST: Basic Statistics of Protein Sequences
NucST: Basic Statistics of Nucleic Acid Sequences
NJdist: Neighbor Joining Phylogeny from Distance Matrix
Utilities (Perl)
mollist: get identifiers list
molrev: reverse DNA sequences
molcat: concatenate sequences
molcut: get partial sequences
molmerge: merge sequences
nuc2ptn: DNA -> Amino acid
rminsdel: remove INS/DEL sites
molcodon: get specified codon sites
molinfo: get varied sites
mol2mol: MOLPHY format beautifer
inl2mol: Interleaved -> MOLPHY
mol2inl: MOLPHY -> Interleaved
mol2phy: MOLPHY -> Sequential
phy2mol: Sequential -> MOLPHY
must2mol: MUST -> MOLPHY

MOLPHY is a free software, and you can use and redistribute it. The programs are written in a standard subset of C with UNIX-like OS. The utilities are written in the "Perl" (Ver.4.036) with UNIX-like OS. MOLPHY has been tested on SUN4's (cc & gcc with SUN-OS 4.1.3) and HP9000/700 (cc, c89 & gcc with HP-UX 9.05).
However, MOLPHY has NOT been tested on VAX, IBM-PC, and Macintosh.

NETWORK DISTRIBUTION ONLY: The latest version of MOLPHY is always available by anonymous ftp in /pub/ISMLIB/MOLPHY/.
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Updated Feb 13 , 2004