A synteny-based method that is flexible enough to handle a model of evolution involving whole genome duplication events, in addition to rearrangements, gene insertions, and losses. Ancestral relationships between markers are defined in term of Gapped Adjacencies, i.e. pairs of markers separated by up to a given number of markers. It improves on a previous restricted to direct adjacencies, which revealed a high accuracy for adjacency prediction, but with the drawback of being overly conservative, i.e. of generating a large number of contiguous ancestral regions (CARs).

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zakari

hello everyone, I am new in the community and I want to make an analysis that compares three PROCARS, GapAdj and Intercars, so I ask your help if you please

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GapAdj classification

GapAdj specifications

Software type:
Package
Restrictions to use:
None
Output data:
An ancestral genome at node ν
Computer skills:
Advanced
Interface:
Command line interface
Input data:
A set Γ of m modern genomes, a species tree S with leaves labeled with genomes from Γ, and an internal node ν of S representing a speciation event of interest
Operating system:
Unix/Linux
Stability:
Stable

Publications

  • (Gagnon et al., 2012) A flexible ancestral genome reconstruction method based on gapped adjacencies. BMC bioinformatics.
    PMID: 23281872

GapAdj support

Maintainer

Credits

Institution(s)

Département d’Informatique (DIRO), Université de Montréal, Montréal, Canada; McGill Centre for Bioinformatics, McGill University, Montréal, Canada

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