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MOLPHY is a program package for MOLecular PHYlogenetics. It contains several C and Perl programs. The C programs are:

  • 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
The Perl Utilities are:
  • 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 3rd(1st,2nd) codons
  • molinfo: get (non)infomation sites
  • mol2mol: MOLPHY format beautifer
  • inl2mol: Interleaved -> MOLPHY
  • mol2inl: MOLPHY -> Interleaved
  • mol2phy: MOLPHY -> Sequential
  • phy2mol: Sequential -> MOLPHY
  • must2mol: MUST -> MOLPHY

Current Version:   2.2 (2.3 beta 3)

License Type:   Free

Home Site: (Linux binary)

Source Code Availability:   Yes

Available Binary Packages:

  • Debian Package:   No
  • RedHat RPM Package:   No
  • Other Packages:   Yes

Targeted Platforms:

UNIX-like OS, Tested on SUN-OS, HP-UX, Linux

Software/Hardware Requirements:

C compiler and Perl

Other Links:

Mailing Lists/USENET News Groups:


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