WORK IN PROGRESS
PEGP (protein evolutionary genomics pipeline). A software tool for
- protein homology search
- phylogenetic tree construction with annotations (taxonomy, domain architecture, genome context)
- reconstruction of phyletic pattern with identification of paralogs
- CD-HIT
- https://github.com/weizhongli/cdhit/wiki/2.-Installation - installation
- MAFFT
- https://mafft.cbrc.jp/alignment/software/linux.html - installation (recommend usinf .deb for installation)
- trimAl v1.2
conda install -c bioconda trimal
- hmmer
conda install -c bioconda hmmer
- iqtree v2.x
conda install -c bioconda iqtree
- python 3.10
- biopython
conda install biopython
- ete3
conda install -c etetoolkit ete3
- matplotlib
conda install matplotlib
- numpy, pandas, seaborn
conda install seaborn
- prettytable
conda install prettytable
- colorama
conda install colorama
git clone https://github.com/stovc/pegp
- Run
bash utility_scripts/mk_pfam.sh
from the root of the repo