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Phylonco v1.2.0
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@walterxie walterxie released this 25 Sep 04:27
· 35 commits to master since this release
v1.2.0
b50de88

Requirements

BEAST

  • BEAST version 2.7.6 or greater
  • BEASTLabs version 2.0.2 or greater

LPhy and LPhyBeast

  • LPhy version 1.6.0 or greater
  • LPhyBeast version 1.2.0 or greater

LPhy examples: phylonco-lphy-1.2.0-examples.zip

LPhy documentation: phylonco-lphy doc

Release notes

BEAST

  • Coalescent model with Gompertz population growth (f0 and t50 parameterizations)
  • Coalescent model with logistic population growth
  • Coalescent model with model averaging by stochastic variable selection (constant, exponential, logistic, Gompertz)
  • Phylonco is now split into separate releases for beast, lphy and lphybeast
  • Fix version compatibility issue with LPhy and LPhyBeast
  • Build now uses Maven instead of Gradle
  • Gompertz example manually patched

LPhy and LPhyBeast

  • haploid function for converting genotypes to haploid alleles
  • LPhyBeast to XML converters for coalescent population function models and model averaging
  • Some LPhy examples manually patched

Setup instructions

The phylonco (beast) and phylonco.lphybeast (lphybeast) packages can be installed using Beauti package manager.

For LPhy installation, the two jars phylonco-lphy-1.2.0.jar and phylonco-lphy-studio-1.2.0.jar need to be copied to the lib subdirectory of your LPhy installation. See setup instructions and the extension installation guide.

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