DeCoSTAR

DeCoSTAR is a software tool to reconstruct ancestral gene organizations of genomes using reconciled phylogenies to study links among genes. The DeCoSTAR algorithm outputs lists of inferred adjacencies in ancestral species or an adjacency forest, and DeCoSTAR is also applicable for inference of adjacencies in extant species.

Topic

Genomics;Phylogeny;Evolutionary biology

Detail

  • Operation: Phylogenetic tree analysis

  • Software interface: Command-line user interface

  • Language: C++

  • License: CeCILL

  • Cost: Free

  • Version name: -

  • Credit: The Agence Nationale pour la Recherche, Ancestrome project.

  • Input: -

  • Output: -

  • Contact: Eric Tannier Eric.Tannier@inria.fr

  • Collection: -

  • Maturity: -

Publications

  • DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies.
  • Duchemin W, Anselmetti Y, Patterson M, Ponty Y, Bérard S, Chauve C, Scornavacca C, Daubin V, Tannier E. DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies. Genome Biol Evol. 2017 May 1;9(5):1312-1319. doi: 10.1093/gbe/evx069. PMID: 28402423; PMCID: PMC5441342.
  • https://doi.org/10.1093/gbe/evx069
  • PMID: 28402423
  • PMC: PMC5441342
  • Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach
  • Chauve C, Ponty Y, Zanetti J. Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. BMC Bioinformatics. 2015;16 Suppl 19(Suppl 19):S6. doi: 10.1186/1471-2105-16-S19-S6. Epub 2015 Dec 16. PMID: 26696141; PMCID: PMC4686788.
  • https://doi.org/10.1186/1471-2105-16-S19-S6
  • PMID: 26696141
  • PMC: PMC4686788
  • Ancestral gene synteny reconstruction improves extant species scaffolding
  • Anselmetti Y, Berry V, Chauve C, Chateau A, Tannier E, Bérard S. Ancestral gene synteny reconstruction improves extant species scaffolding. BMC Genomics. 2015;16 Suppl 10(Suppl 10):S11. doi: 10.1186/1471-2164-16-S10-S11. Epub 2015 Oct 2. PMID: 26450761; PMCID: PMC4603332.
  • https://doi.org/10.1186/1471-2164-16-S10-S11
  • PMID: 26450761
  • PMC: PMC4603332

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