swMATH ID: 29623
Software Authors: Perrin, A., Varré, J.S., Blanquart, S., Ouangraoua, A.
Description: ProCARs: Progressive Reconstruction of Ancestral Gene Orders. Background: In the context of ancestral gene order reconstruction from extant genomes, there exist two main computational approaches: rearrangement-based, and homology-based methods. The rearrangement-based methods consist in minimizing a total rearrangement distance on the branches of a species tree. The homology-based methods consist in the detection of a set of potential ancestral contiguity features, followed by the assembling of these features into Contiguous Ancestral Regions (CARs). Results: In this paper, we present a new homology-based method that uses a progressive approach for both the detection and the assembling of ancestral contiguity features into CARs. The method is based on detecting a set of potential ancestral adjacencies iteratively using the current set of CARs at each step, and constructing CARs progressively using a 2-phase assembling method. Conclusion: We show the usefulness of the method through a reconstruction of the boreoeutherian ancestral gene order, and a comparison with three other homology-based methods: AnGeS, InferCARs and GapAdj. The program, written in Python, and the dataset used in this paper are available at http://bioinfo.lifl.fr/procars/.
Homepage: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460626/
Related Software: ExaBayes; ExaML; MulRF; iGTP; GASTS; MLGO; MrBayes; HyDe; UFBoot2; S-Cluster++; SplitsTree; MCScanX; CYNTENATOR; i-ADHoRe; Blast2GO; PhyloNetworks; MURPAR; StarBEAST2; ALPHA; BitPhylogeny; SciClone
Cited in: 1 Publication

Cited by 1 Author

1 Warnow, Tandy J.

Cited in 1 Serial

1 Computational Biology

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