This script allows you to automate steps of phylogenetic analysis such as:
- proteome downloading from UniProtKB
- Proteins Clustering
- MSA of each cluster in two variants
- Only one protein from each organism
- Many protein from the same organism (paralogous proteins)
- Maximum Likelihood Tree construction for both variants of alignment
- Consensus Tree construction in following variants:
- From all ML-Trees
- Only from trees with high bootstrap confidence level.
- Super Tree construction
The script requires:
If all required execs are in PATH you can simply run:
$ python phylo_pipeline -t taxon_name -o output_dir --og out_group_organism_name