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molphy

Program Package for MOLecular PHYlogenetics

Variants:
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.
Homepage:
Package version:2.3b3-5
Architecture:ia64
Distribution:Debian
Filename:molphy_2.3b3-5_ia64.deb

/usr/share/doc/molphy/README

MOLPHY: A Computer Program Package for Molecular Phylogenetics

Readme
       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
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/usr/share/doc/molphy/README.Debian

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 
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/usr/share/doc/molphy/examples/tests/compare/README.compare

I've got those test examples from 
     http://bioweb.pasteur.fr/docs/doc-gensoft/molphy/testdata
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, test6.mls, test7.mls and test15.nj
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/usr/share/man/man1/mollist.1.gz

MolPhy Utilities(1)                              MolPhy Utilities(1)



NAME
       mollist - get id
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/usr/share/man/man1/protml.1.gz

MolPhy(1)                                                  MolPhy(1)



NAME
       MolPhy - program
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/usr/share/doc/molphy/changelog.Debian.gz

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

  * Added XS-Autobuild: yes

 -- Andreas Tille <tille@debian
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/usr/share/doc/molphy/copyright

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

Hom
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