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 mamba install biopython
• ete3 mamba install -c conda-forge ete3
• matplotlib mamba install matplotlib
• numpy, pandas, seaborn mamba install seaborn
• prettytable mamba install prettytable
• colorama mamba install colorama
• reportlab mamba install conda-forge::reportlab

Installation

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

Running

Download genomes

bash prepare_genomes/download_genome_metadata.sh python3 prepare_genomes/filter_gtdb_metadata.py bash prepare_genomes/download_genomes.sh

Build a database

python3 database_building/make_db GENOMES_FOLDER_PATH METADATA_PATH OUTPUT_DATABASE_PATH sample: python3 database_building/make_db.py test/genomes test/genomes/metadata.tsv databases/test

Run an analysis

run python3 pegp.py

Create a project

For a test project:

n project test/hmms/clpP_TIGR00493.1.HMM

Running the analysis steps

1. s project 1
2. s project 2
3. s project 3
4. s project 4 70 0.05
5. s project 5 0.9
6. s project 6
7. s project 7
8. s project 8
9. s project 9
10. s project 10