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Phylogenetic estimation using Maximum Likelihood

PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test).

PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the “comfort zone” for PhyML generally lies around 3 to 500 sequences less than 2,000 character long.

Package version:2:20100123-1


phyml (2:20100123-1) unstable; urgency=low

  * New upstream release.

  [ Nelson A. de Oliveira ]
  * Fix watch file.
  * Increment the epoch number to fix a typo in the version number.

  [ Charles Plessy ]
  * Checked conformance with Policy 3.8.4 and incremented Standards-Version
    in debian/control to reflect this (no changes needed).
  * Moved the bibliographic reference from debian/refere


Version  date		what has been changed

5.0       26.08.2000    - changes to manual,
                        - cpREV hidden by -DCPREV flag
                        - chi2test, quartio included into source code files
                        - generic scr/Makefile.generic
                        - src/ for VAX
			- AUTHORS, README, ChangeLog updated
			- INSTALL checked


Machine-readable license summary, see ‘’.

Name     :  PhyML
Source   :
Contact  :
	Stephane Guindon <>
	Department of Statistics. University of Auckland. New Zealand
	Universite Montpellier II - CNRS UMR 5506. LIRMM. Montpellier France.
	Olivier Gascuel <>

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