MolPhy Utilities - program package for MOLecular PHYlogenetics

The Molphy package includes several Perl utilities:

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

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]

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.

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