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PhyChro

PhyChro: Phylogenetic reconstruction based on Chromosomal rearrangement signal (synteny block adjacencies).

Overview:

PhyChro is a tree reconstruction method solely based on chromosomal rearrangement data that can be applied to a wide range of eukaryotic genomes with different gene contents and different levels of synteny conservation. PhyChro uses a reconstruction principle that differs from the usual methods based on distance, parsimony, maximum likelihood or quartet. The principle here is to repeatedly (i.e. for each synteny breakpoint) split the set of genomes into two disjoint groups corresponding to incompatible gene adjacencies. Then, tree reconstruction is achieved through a bottom-up approach by hierarchically grouping sister-genomes that minimize the number of incompatible adjacencies. PhyChro estimates branch lengths based on the level of chromosomal rearrangements and provides confidence scores for each branch of the tree.

Downloads

1. If it is the first time you use/download a CHROnicle program, you need to download the CHROnicle architecture, which contains toy examples as well as scripts that converts EMBL, GenBank or Fasta files into the expected SynChro input format. If you already used another CHROnicle tool, you may skip this step.

2. You then need to download the PhyChro program and to add it to your CHROnicle/Programs/ directory:

Not yet available - Waiting for the publication of the algorithm

Please take a look at the README file for usage instructions.

3. You then need to download the SynChro program too, if you want to reconstruct trees directly from EMBL/GenBank/Fasta files (see the SynChro' page). However, if you want to run PhyChro on different pairwise synteny blocks, notice that they have to be formatted into the expected format (look at the README file for details).

Quick start

1. Compute synteny blocks with SynChro. In the CHROnicle/Programs/1SynChro/ directory, type the following command:

./SynChro.py Yeast 2 0

Look at the SynChro's webpage for details.


2. Reconstruct the phylogenetic tree with PhyChro. In the CHROnicle/Programs/2PhyChro/ directory, type the following command:

./PhyChro.py Yeast 2 tree1 0

It will recontruct the tree for all genomes (the .def files) present in the CHROnicle/Yeast/01Genomes/ directory using the synteny blocks (the .orth.pairs and .orth.synt files) present in the CHROnicle/Yeast/11Blocks/Delta2/ directory. To reconstruct only a sub-tree, change the 0 into 1 in the command line. The resulting tree is written in CHROnicle/Yeast/20Trees/Delta2/tree1.outtree (in the newick format).


3. Reconstruct the phylogenetic tree with PhyML. Type the following command:

./PhyMut.sh Yeast 3 80

It will recontruct the tree with PhyML, for all genomes present in the CHROnicle/Yeast/01Genomes/ directory. To do so, it uses the synteny blocks present in the CHROnicle/Yeast/11Blocks/Delta3/ directory to identify families of syntenic homologs, with a average of similarity bigger than 80% (computed with the script InterOrtho.py, see SynChro' page), which are then align to be used as input for PhyML. The results (gene families, alignments, concatenation file, PhyML's tree) are written in the CHROnicle/Yeast/12OrthFamilies/Delta3/ directory.

Contact

For questions, comments, or suggestions feel free to contact Guénola Drillon.

Reference

  • Drillon G, Fischer G and Carbone A (2015) Phylogenetic reconstruction based on synteny block and gene adjacencies. (re)submitted at Systematic Biology.

Last Update January 2016