Prunier 1.0

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

Abby S.S., Tannier E., Gouy M. and Daubin V. 2010. BMC Bioinformatics.

Prunier aims at detecting lateral gene transfers in a gene tree given a species tree.

Input:
- a bifurcating species tree (Newick format) rooted or not,
- a gene alignment (PHYLIP interleaved or FASTA format),
- an optional bifurcating gene tree with support values (Newick format). Note that to be consistent with Prunier, the gene tree has to be estimated with the same parameters than used for branch length estimation of the reference species tree (i.e. WAG+G8+I for proteic alignment, and GTR+G8+I for nucleic alignment).
Output: a scenario of lateral gene transfers
- per possible rootings of the species tree.
Prunier builds a gene tree (if not provided by the user) and estimates branch lengths of the species tree using Treefinder [1].
Two versions of Prunier's algorithm can be run.
- A “Fast” version that grounds on support values (LR-ELW values provided by Treefinder if the gene tree is not user-defined).
- A “Slow” version that uses the ELW test [2].
Prunier is implemented in C++ and uses the Bio++ library [3].

Prunier's performances

Prunier was tested on a simulated dataset available here. Prunier was designed to deal with real datasets, and was tested on maximum-likelihood (ML) gene trees. Prunier was compared to two programs, EEEP [4] and RIATA-HGT [5] that deal with the same biological problem, i.e. the reconciliation of a rooted reference tree with unrooted gene trees that are not necessary fully resolved. See Prunier's article for further details.

Installation

Prunier drives the Treefinder program to do ML tests (Slow version), to build ML gene trees (if not provided by the user) and to estimate branch lengths of the reference tree given the gene alignment (if needed for computations).
Please install the Treefinder program before running Prunier in any directory of your PATH environment variable so that Prunier can run it. Then download below the appropriate binary of Prunier, and make it executable.

Download Prunier

MacOS X

64-bit Linux on x86

Documentation

Run Prunier using the command-line. Prunier's usage is described when typing the name of the binary.
Prunier's mandatory arguments are:

input.tree.file: your reference (species) tree
aln.file: your alignment file

Prunier's optional arguments, and corresponding [default values] are:

genetree.file[=NA]: a bootstrapped gene tree file. Prunier can deal with gene trees containing only a subset of the species found in the reference tree.
sequence.type[=prot]: sequence type. Other possible value: dna
aln.type[=PHYLIP]: format of the provided alignment. Default is Phylip interleaved. Other possible value: FASTA
method.name[=Fast]: version of Prunier to run. Other possible value: Slow
boot.thresh.conflict[=90]: support value threshold for topological conflict.
test.thresh[=0.05]: p-value threshold for significant conflict with the ELW test (Slow version).
norm.bp[=100]: range of support values in the gene tree file. Default is between 0 and 100.

Examples of Prunier's command-line (example files are available here):

Prunier input.tree.file=alpha_concat_root_reduced.tree aln.file=seqdata1.fas.phy >& prunier_result_simul1

Prunier input.tree.file=alpha_concat_root_reduced.tree aln.file=seqdata110.fas.phy genetree.file=seqdata110.fas.phy_tf.tree method.name=Slow >& prunier_result_simul110

NB: the standard error and outputs have been directed into the file prunier_result_simul1. Please note that Prunier would be soon able to write its results into a file provided by the user.

Bibliography

[1] Jobb, G., von Haeseler A. , and Strimmer, K. TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics. 2004. BMC Evolutionary Biology.
[2] Strimmer K. and Rambaut A. Inferring confidence sets of possibly misspecified gene trees. 2002. Proc Biol Sci.
[3] Dutheil J., Gaillard S., Bazin E., Glémin S., Ranwez V., Galtier N. and Belkhir K. Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. 2006. BMC Bioinformatics.
[4] Beiko R.G. and Hamilton N. Phylogenetic identification of lateral genetic transfer events. 2006. BMC Evolutionary Biology.
[5] Than C. and Nakhleh L. SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions. 2008. APBC.

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