PHYML_MULTI

phyml_multi, derived from PhyML,
A simple, fast, and accurate algorithm to estimate
large phylogenies by maximum likelihood.

Stephane Guindon and Olivier Gascuel,
Systematic Biology 52(5):696-704, 2003.
Please cite this paper if you use this software in your publications.

How to compile PhyML_multi ?

Linux or Solaris (with gcc)

. 'cd' to the sources directory, . type 'make'

OSX (Jaguar or Panther)

. 'cd' to the sources directory . remove the option '-static' from the CFLAGS . type 'make'

Usage

Command line use

phyml_multi [ sequences data_type format data_sets bootstrap_sets model [kappa] invar nb_categ alpha tree opt_topology opt_lengths use_HMM nb of trees ]

You can use phyml_multi with no arguments, in this case change the value of a parameter by typing its corresponding character as shown on screen.

You can alternatively use phyml_multi with the following arguments :

• sequence_file DNA or Amino-Acids sequence filename (PHYLIP format)

• data type 0 = DNA | 1 = Amino-Acids

• format i = interleaved sequence format | s = sequential

• data_sets number of data sets to analyse (ex:3)

• bootstrap_sets number of bootstrap data sets to generate (ex:2) only works with one data set to analyse

• model substitution model name JC69 | K2P | F81 | HKY | F84 | TN93 (DNA) JTT | MtREV | Dayhoff | WAG (Amino-Acids)

• kappa transition/transversion ratio, only for DNA sequences, a fixed value (ex:4.0) | e to get the maximum likelihood estimate

• invar proportion of invariable sites, a fixed value (ex:0.0) | e to get the maximum likelihood estimate

• nb_categ number of relative substitution rate categories (ex:4)

• alpha gamma distribution parameter, a fixed value (ex:1.0) | e to get the maximum likelihood estimate

• tree starting tree filename (Newick format), your tree filename | BIONJ for a distance-based tree

• opt_topology optimise tree topology ? y | n

• opt_lengths optimise branch lengths and rate parameters ? y | n

• use_HMM use HMM ? n | y

• number of trees How many trees (ex:4) ?

Examples

.DNA sequences, no HMM : ./phyml_multi seqs1 0 i 2 0 HKY 4.0 e 1 1.0 BIONJ y n n 2

.AA sequences, HMM : ./phyml_multi seqs2 1 i 1 5 JTT 0.0 4 1.0 BIONJ n n y 3

Posterior analysis

Posterior analysis of phyml_multi reconstruction needs either to run PartitioningHMM.py for HMM or PartitioningMM.py for maximum predictive partitioning.

These files need the installation of SARMENT libraries, there.

Example

The file simSeq.phy contains an example alignment in which a recombination event occured. This is one of the simulated alignments as found in the "Evolutionary Bioinformatics" article. The breakpoint should be found at position 599. To use phyml_multi, type:

For use with the phylo-HMM:

phyml_multi simSeqs.phy 0 i 1 0 HKY e e 4 e BIONJ y y y 2

and then to see the segmentation (with SARMENT library):

python3 PartitioningHMM.py simSeqs.phy_phyml_siteLks.txt 0.997973 or : python3 PartitioningMM.py simSeqs.phy_phyml_siteLks.txt

For use with the mixture model: phyml_multi simSeqs.phy 0 i 1 0 HKY e e 4 e BIONJ y y n 2

and then to see the segmentation: python3 PartitioningMM.py simSeqs.phy_phyml_siteLks.txt

This should give you the right answer, in a matter of a few minutes on a single desktop computer.

For any question, contact bastien.boussau@univ-lyon1.fr

Reference

Boussau B, Guéguen L, Gouy M. A mixture model and a hidden markov model to simultaneously detect recombination breakpoints and reconstruct phylogenies. Evol Bioinform Online. 2009 Jun 25;5:67-79. d oi: 10.4137/ebo.s2242. PMID: 19812727; PMCID: PMC2747125.