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MolPhy Utilities

MolPhy Utilities

Section: User Commands (1) Updated: November 7, 2001
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NAME

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
int2mol - Interleaved -> MOLPHY
mol2int - MOLPHY -> Interleaved
mol2phy - MOLPHY -> Sequential
phy2mol - Sequential -> MOLPHY
must2mol - MUST -> MOLPHY
many more perl conversion utilities which are not further described

 

SYNOPSIS

MolPhy Utilities is a program package for MOLecular PHYlogenetics which includes several Perl utilities:

mollist [sequence_file]
molrev [sequence_file]
molcat [sequence_file]
molcut [sequence_file]
molmerge [sequence_file]
nuc2ptn [switches] [sequence_file]
rminsdel [switches] [sequence_file]
molcodon [sequence_file]
molinfo [switches] [sequence_file]
mol2mol [sequence_file]
inl2mol [sequence_file]
mol2int [sequence_file]
mol2phy [sequence_file]
phy2mol [sequence_file]
must2mol [sequence_file]
ali2mol [sequence_file]
clus2mol [sequence_file]
degene4l [switches] [sequence_file]
degene4 [switches] [sequence_file]
disjoint [sequence_file]
dna2ami [options] [no_align_files]
eali2mol [EMBL_ALIGN_file]
egetcds [EMBL_file]
getcds [EMBL_file]
egetcds [Genbank_file]
info2mol [sequence_file]
infocode [switches] [sequence_file]
infocode [switches] [sequence_file]
mc2mol [sequence_file]
mega2mol [sequence_file]
mol2info [sequence_file]
mol2seq [sequence_file]
molcons [sequence_file]
molsplit [sequence_file]
njt2tpl [machine_readable_tree_with_branch_length]
mol2mol [sequence_file]
nuc2NUC [sequence_file]
rmid3 [switches] [sequence_file]
rmleu [switches] [sequence_file]
rmsyno [switches] [sequence_file]
seq2mol [sequence_file]
seqwrap [file]

 

DESCRIPTION

This is the Debian GNU/Linux version of 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.

The perl utilities above are usefull to convert different formats of phylogenetic data.

 

AUTHOR

This manual page was written by Andreas Tille <tille@debian.org>, for the Debian GNU/Linux system (but may be used by others).


 

Index

NAME
SYNOPSIS
DESCRIPTION
AUTHOR

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Time: 21:23:47 GMT, April 16, 2011