viral-phylogeny

Phyloformer

Install mamba if you want to use it instead of conda

conda install -n base -c conda-forge mamba

Clone the phyloformer repo

git clone https://github.com/lucanest/Phyloformer.git && cd Phyloformer

Create the virtual env and install the phyloformer package inside

conda create -n phylo python=3.9 -c defaults && conda activate phylo pip install -r requirements.txt

Generate the distance matrix (Change the code)

python infer_alns.py -o data/testdata/pf_matrices models/pf.ckpt data/testdata/msas

Generate tree from generated matrix

./bin/bin_macos/fastme -i "data/pf66_matrices/PF00066.phy" -o "data/pf66_matrices/PF00066.nwk" --nni --spr

MSA Transformer

Install MsaPhylo

git clone https://github.com/Cassie818/MsaPhylo.git cd MsaPhylo

Install prerequisite packages

pip install fair-esm --quiet pip install transformers --quiet pip install pysam --quiet pip install Bio pip install ete3

Run the model

python MsaPhylo.py --i "./data/Pfam/PF00066.fasta"
--name 'PF00066'
--o "./PF00066_output_tree"
--l 2

CMAPLE

PhyloGFN