- biopython
- PhyML
- RAxML compiled with the PTHREADS lib
pip install biopython
brew install phyml raxml
git clone https://github.com/chrisgulvik/phylogenetics_scripts.git $HOME/phylogenetics_scripts
echo 'export PATH="$PATH:$HOME/phylogenetics_scripts"' >> $HOME/.bash_profile
-
Build a ML tree using make_ML_tree.py
make_ML_tree.py -f input.fasta.aln -e .fasta.aln -T 15 -
Filter for only variant sites with remove_uninformative_sites.py
remove_uninformative_sites.py -i input.fasta.aln