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.
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.
Contains Python scripts called in bash scripts above
- astral-bp-trees : species trees estimated by running ASTRAL_BP
- astrid-bp-trees : species trees estimated by running ASTRID_BP
- input-data-sets : retroelement insertion data sets simulated with ms
- mdc-bp-trees : species trees estimated by running MDC_BP
- model-trees : true species trees used to simulate retroelement insertion data sets
- parsimony-trees : species trees estimated by running variants of parsimony (unordered, Camin-Sokal, and Dollo)
- data-branch-info.csv : branch lengths estimated with ASTRAL_BP and related data (see README)
- data-species-tree-error.csv : species tree error for all methods and all data sets (see README)
- data-species-tree-error-collapsed.csv : species tree error for ASTRAL_BP collapsing branches based on their support values (see README)
Contains Python scripts for organizing data (see csvs directory ), writing tables in Latex (see tables directory), and plotting data (see plots directory)
Our experimental study uses several external packages:
- ASTRAL v5.7.5 [download] [paper]
- ASTRID v2.2.1 [download] [paper]
- PAUP* v4a168 [download]
- PhyloNet v3.8.2 [download] [paper]
- PRANC [download] [paper]