stovc/pegp

PEGP (protein evolutionary genomics pipeline). A software tool for protein homology search, phylogenetic tree construction with annotations (taxonomy, domain architecture, genome context), and reconstruction of phyletic pattern with identification of paralogs

Python

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