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TREE-QMC-v1 Tutorial

Step 1: Clone TREE-QMC repository.

git clone https://github.com/molloy-lab/TREE-QMC-v1.git

Step 2: Build TREE-QMC.

cd TREE-QMC-v1/MQLib
make
cd ..
g++ -std=c++11 -O2 -I MQLib/include -o TREE-QMC-v1 src/TREE-QMC.cpp MQLib/bin/MQLib.a

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

./TREE-QMC-v1 -i example/avian_uce_trees_3679.tre -o example/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 
java -jar ASTRAL/Astral/astral.*.jar -q example/treeqmc.tre -i example/avian_uce_trees_3679.tre -o example/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.