ProCARs

What is ProCARs ?

ProCARs is a program used to reconstruct Ancestral gene orders as CARs (Contiguous Ancestral Regions) with a progressive homology-based method. The method runs from a phylogeny tree (without branch lengths needed) with a marked ancestor and a block file.

This homology-based method is based on iteratively detecting and assembling ancestral adjacencies, while allowing some micro-rearrangements of synteny blocks at the extremities of the progressively assembled CARs.

The method starts with a set of blocks as the initial set of CARs, and detects iteratively the potential ancestral adjacencies between extremities of CARs, while building up the CARs progressively by adding, at each step, new non-conflicting adjacencies that induce the less homoplasy phenomenon. The species tree is used, in some additional internal steps, to compute a score for the remaining conflicting adjacencies, and to detect other reliable adjacencies, in order to reach completely assembled ancestral genomes.

Download

ProCARs has been developed with Python 2.7.5.

You can download it and install it on your server with the following link. Please consult the enclosed README.md file for information about installing and running ProCARs. You can also find this information, as well as many others (formats of the input and output files, etc.) in the ProCARs Documentation (also enclosed with ProCARs package).

ProCARs is released under a CeCILL-B licence (a GPL-compliant licence).

Reference

ProCARs: Progressive Reconstruction of Ancestral Gene Orders
Perrin A., Varré J.S., Blanquart S. and Ouangraoua A.
BMC genomics (ISCB-LA), vol 16, 2015.

Amniotes dataset

You can here download the dataset we used to reconstruct the Boreoeutherian ancestor (Phylogenic tree and Orthologous blocks) with ProCARs. These files are also provided with the ProCARs package (see Downloading ProCARs), in the Examples/Boreoeutherian_ancestor directory.
You will also find the results found by ProCARs and three other homology-based methods: AnGeS, InferCARs and GapAdj. There is as well a graphical representation of those 4 reconstructed ancestors, showing the human chromosomal syntenies (additional_file2.pdf).

• Phylogenetic tree: tree_boreoeutherian_ancestor.ph and additional_file1.pdf
• Orthologous blocks: orthology_blocks.txt
• Boreoeutherian ancestor build by:
  • ProCARs: Ancestor_ProCARs.txt
  • AnGeS: Ancestor_Anges.txt
  • InferCARs: Ancestor_InferCARs.txt
  • GapAdj (0.79, 3): Ancestor_GapAdj.txt
• Human chromosomal syntenies: additional_file2.pdf