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FYI: You can use TREE-QMC to estimate species trees and estimate support from retroelement insertion presence/absence matrices via quartets. Use command:

treeqmc --bp --support -i <input matrix> 

This repository contains data sets and scripts used in the study, ``Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone.''

The Python script to run ASTRAL_BP is here; it requires TreeSwift as a dependency.

scripts directory

Contains bash scripts for

  • a : running parsimony methods
  • b : running ASTRAL_BP
  • c : running ASTRID_BP and MDC_BP
  • d : computing species tree error (writes CSV file)
  • e : collapsing branches based on some threshold for branch support and then computing species tree error (writes CSV file)
  • f : extracting branch lengths and related data from newick strings (writes CSV file)
  • g : running ASTRAL_BP and re-rooting at chicken outgroup for Palaeognathae analysis
  • h-i : analyzing ASTRAL_BP trees from step (g) with 1000-5000 simulated retroelement insertions

Note that the scripts for the ms simulation and the species trees estimated using SDPquartets and Dollo parsimony are available on Dryad.

tools directory

Contains Python scripts called in bash scripts above

data directory

summary directory

Contains Python scripts for organizing data (see csvs directory ), writing tables in Latex (see tables directory), and plotting data (see plots directory)

external software

Our experimental study uses several external packages:

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