Table 1 Tools, databases and tutorials relevant for the identification and characterization of the host-pathogen share-ome. All URLs were accessible as of January 2021

NCBI Entrez Databases

http://www.ncbi.nlm.nih.gov

NCBI Entrez Protein Database

http://www.ncbi.nlm.nih.gov/protein

NCBI Entrez Taxonomy Database

http://www.ncbi.nlm.nih.gov/taxonomy

STRING Viruses database

http://viruses.string-db.org/; version 11.0

CD-HIT

http://weizhongli-lab.org/cd-hit/

E-Utilities esearch-efetch

https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Demonstration_Programs

entrezEsearch

https://github.com/gwatiyapJ/SiMiLyG

kmerslicer

https://github.com/gwatiyapJ/SiMiLyG

Unipro UGENE tools

http://ugene.net/

UniProt Retrieving and ID Mapping tool

https://www.uniprot.org/uploadlists/

CateGorizer

https://www.animalgenome.org/tools/catego/

Unix utilities

https://unix.stackexchange.com/

Tutorial 1: Notes on how to use R for doing statistical analysis and graphics

https://cran.r-project.org/manuals.html

Tutorial 2: Unipro UGENE Manual Version 37, 2020. Consists of user guide to bioinformatics tools for alignments, genome sequencing, data analysis, and amino acids sequence visualization, among others.

http://ugene.net/downloads/UniproUGENE_UserManual.pdf

Tutorial 3: User’s guides on implementation for removing duplicates sequences and generating representative sequences

http://www.bioinformatics.org/cd-hit/cd-hit-user-guide.pdf

Tutorial 4: Webinar: Introduction to NCBI’s E-utilities API

https://www.youtube.com/watch?v=iCFVVexp30o&t=2561s