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Make a pipeline for phylogeny #1

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pveber opened this issue Jan 31, 2016 · 0 comments
Open
20 tasks

Make a pipeline for phylogeny #1

pveber opened this issue Jan 31, 2016 · 0 comments

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@pveber
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pveber commented Jan 31, 2016

Suggestion for a phylogenetic pipeline by @Boussau:

Items of the same level are alternatives

clustering:

  • blast then
    • orthomcl
    • silix (+hifix)

alignement:

  • mafft
  • clustal-omega
  • muscle
  • prank
  • Saté
  • Pasta

gene phylogeny:

  • PhyML
  • RaxML
  • IQTree
  • GARLI
  • mrBayes
  • Paup
  • Beast
  • fasttree
  • revBayes

species phylogeny:

  • MPEst
  • Astral
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@pveber