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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. Other programs (C language) 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 etc.
Package version:2.3b3-5


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 ac


molphy for DEBIAN

Because there are no upstream changes since 5 years I consider the
project to be dead.  Anyway it is used in Arb which I want to package
I build this package separately.  Thus I also applied all patches
from Arb.

Molphy uses a strange source philosophy.  In the original Makefile
some source files are forced to be a copy of some others.  The 
different targets 


I've got those test examples from
The original files in the compare directory where build with molphy 2.2.
I found out that the results with version 2.3b3 differ slightly in
the precision of some floats.  I think this is OK. 

On the other hand there were some different trees created in 
   test4.nj,, and test15.nj


MolPhy Utilities(1)                              MolPhy Utilities(1)

       mollist - get id


MolPhy(1)                                                  MolPhy(1)

       MolPhy - program


molphy (2.3b3-5) unstable; urgency=low

  * Added XS-Autobuild: yes

 -- Andreas Tille <tille@debian


This package was debianized by Andreas Tille <>
Mon,  5 Nov 2001 23:50:39 +0100


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