Snakemake workflow to create phylogenetic trees using supertree and supermatrix approach from gene sequences in fasta format.
The workflow conducts the following steps:
- Multiple sequence alignment using MAFFT (https://github.com/GSLBiotech/mafft)
- Alignment trimming with ClipKIT (https://github.com/JLSteenwyk/ClipKIT)
- Genetree creation using IQ-TREE (https://github.com/Cibiv/IQ-TREE)
- Supertree creation with ASTRAL (https://github.com/smirarab/ASTRAL)
Clone the repository:
git clone https://github.com/LKress/snakephylo.git
cd snakephylo
Install snakemake (see https://snakemake.readthedocs.io/en/stable/getting_started/installation.html)
conda create -n snakemake -c conda-forge -c bioconda snakemake
Install conda environments (for workdir setup check section Usage)
snakemake --cores 2 --use-conda --conda-create-envs-only --directory /path/to/workdir
Create a workdirectory with the following directory structure:
<workdir>/
├── data/
├── <dataset1>/
│ ├── <gene1>.fasta
│ ├── <gene2>.fasta
├── <dataset2>/
├── <gene1>.fasta
├── <gene2>.fasta
All names in in brackets (<>) can be chosen freely.
To run a dry run execute:
snakemake --cores 2 --use-conda --directory /path/to/workdir -n
To execute the pipeline:
snakemake --cores 2 --use-conda --directory /path/to/workdir
The resulting supertree is stored at /path/to/workdir/results/trees/SUPERTREE.nwk.
It can be viewed e. g. on https://itol.embl.de/.