WORK IN PROGRESS

pegp

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

Dependencies

Software

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 packages

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

Installation

git clone https://github.com/stovc/pegp
Run bash utility_scripts/mk_pfam.sh from the root of the repo