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