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Options to create gene trees and species tree
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@ecbush ecbush released this 29 Jul 23:46
· 209 commits to master since this release
2.2.0
e6ea88d
  • Added makeSpeciesTree option. This makes gene trees for the hard core set of gene families (using FastTree with GTR+CAT) and then combines them into a species tree using ASTRAL. There is also makeGeneFamilyTrees to make gene trees for the families.
  • Several changes to internal objects and processes to facilitate running larger numbers of strains.
  • parseGenbank can now optionally create DNA files (depending on the new parameter dnaBasedGeneTrees).
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