This section includes notes and code for comparative genomics analyses.

Table of contents

1. Phylogeny
   1. Fold-Tree

Phylogeny

Fold-Tree

Paper GitHub

First, let’s create a conda environment to run Proteinortho:

git clone https://github.com/DessimozLab/fold_tree.git
cd fold_tree
conda env create -n foldtree --file=workflow/config/foldtree.yaml
conda activate foldtree

Brief instructions on how to run the analysis on a custom set of proteins:

Make a myfam project directory:

mkdir myfam

Inside of myfam create a sequence_dataset.csv file:

gene_id1.pdb
gene_id2.pdb
...
gene_idN.pdb

Finally, run the snamemake workflow:

snakemake --cores 16 --use-conda -s workflow/fold_tree --config folder=myfam filter=False foldseek_cores=16 custom_structs=True