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Inconsistency of species-tree methods under gene flow

Scripts for simulation study on Syst Bio paper: Solís-Lemus, C., Yang, M. and Ané, C. Inconsistency of species-tree methods under gene flow

scripts

true gene trees analyses

The scripts will simulate gene trees with ms on a given species tree, and then use the simulated gene trees as input in ASTRAL, NJst and PhyloNet to estimate the species tree.

  • Follow the steps in the README file inside scripts/trueGeneTrees.

  • Links to Astral, NJst, ms and PhyloNet in the README file as well.

estimated gene trees analyses

The scripts will use the simulated gene trees from the true gene trees analyses, and simulate DNA sequences with Seq-Gen. Then, use RAxML to estimate gene trees, and use the estimated gene trees as input in Astral, NJst and PhyloNet.

  • Follow the steps in the README file inside scripts/estGeneTrees

  • Links to Astral, NJst, PhyloNet, Seq-Gen and RAxML in the README file as well.