README.md

TREE-QMC Tutorial

Step 1: Clone TREE-QMC repository.

git clone https://github.com/molloy-lab/TREE-QMC.git

Step 2: Build TREE-QMC.

cd TREE-QMC
cd MQLib
make
cd ..
g++ -std=c++11 -O2 -I MQLib/include -o TREE-QMC src/*.cpp MQLib/bin/MQLib.a

Step 3: Run TREE-QMC on the example input data.

cd tutorial
../TREE-QMC -i avian_uce_trees_3679.tre -o treeqmc.tre

This should take no more than a few minutes. Note: The example data file contains the best ML (RAxML) UCE trees from the Avian Phylogenomics Project.

Step 4: Branch lengths and support values can be estimated using ASTRAL with the following commands.

git clone https://github.com/smirarab/ASTRAL.git
cd ASTRAL
unzip Astral.*.zip
cd ..
java -jar ASTRAL/Astral/astral.*.jar -q treeqmc.tre -i avian_uce_trees_3679.tre -o treeqmc_with_support.tre 

In the future, we plan to implement these calculations within TREE-QMC for ease of use. Note: The root of the tree is (TINMA,STRCA) -- see the provided name map for more information.