Archive // Education & Computational Resources

Education & Tools

A centralized repository of bioinformatic workflows, educational materials, and computational tools developed at VEE Lab. All assets follow open science principles.

VEE Tools

02 Tools

Gmeta Toolkit

GitHub

A toolkit for recover and management of genome metadata, streamlining the annotation and curation of genomic datasets for ecological and evolutionary analyses.

Metadata Genomics Annotation

ArchaeaHQ

V1.0

A database of high quality archaeal genomes linked with curated environmental information.

Archaea Genomics Database

Protocols

19 Entries

description Protocolunfold_more	schedule Last Modifiedunfold_more	notes Summaryunfold_more	label Typeunfold_more	link Websiteunfold_more	menu_book Referenceunfold_more
DefenseFinder	March 28, 2026	Identification of defense systems in bacterial and archaeal genomes	Defense Systems	defensefinder.mdmlab.fr	Tesson et al. 2022
BLASTn	March 31, 2026	Create a database and search for homologues in nucleotide FASTA files	Sequence Search	blast.ncbi.nlm.nih.gov	Altschul et al. 1990
Barrnap	March 31, 2026	rRNA prediction in bacterial, archaeal, and fungal genomes	Annotation	github.com/tseemann/barrnap	—
Bedtools	March 31, 2026	Edit and extract information from FASTA and BED files	Sequence	bedtools.readthedocs.io	Quinlan & Hall 2010
CheckM	March 31, 2026	Check genome completeness and contamination using marker gene sets	Bin Cleaning Quality	github.com/Ecogenomics/CheckM	Parks et al. 2015
ClipKIT	March 31, 2026	Trim sequence alignments with smart, parsimony-informed gap removal	Alignment	github.com/JLSteenwyk/ClipKIT	Steenwyk et al. 2020
ColabFold	March 31, 2026	Predict protein structures using AlphaFold2 locally or via Google Colab	Structure	github.com/sokrypton/ColabFold	Mirdita et al. 2022
CheckV	June 20, 2025	Assess quality of metagenome-assembled viral genomes	Virus Annotation	checkv.readthedocs.io	Nayfach et al. 2021
DIAMOND BLAST	April 01, 2026	Create a database and search for homologues in amino acid FASTA files	Sequence Search	github.com/bbuchfink/diamond	Buchfink et al. 2021
EMBOSS cusp	April 3, 2026	Codon usage prediction from nucleotide sequences	Annotation	emboss.sourceforge.net	—
FoldSeek	April 3, 2026	Search proteins for structural homologues using fast 3D structure alignment	Protein Structure	search.foldseek.com	van Kempen et al. 2023
geNomad	April 3, 2026	Recover mobile genetic element sequences from metagenomes using a neural network-based classifier	Virus	portal.nersc.gov/genomad	Camargo et al. 2023
HMMER	April 3, 2026	Protein homology search using profile hidden Markov models	Annotation	github.com/EddyRivasLab/hmmer	Eddy 2011
InterProScan	April 3, 2026	Protein domain annotation using integrated signature databases	Annotation	interproscan-docs.readthedocs.io	Jones et al. 2014
MMseqs2	April 3, 2026	Cluster proteins by sequence similarity at high speed and sensitivity	Protein	github.com/soedinglab/mmseqs2	Steinegger & Söding 2017
MinCED	April 3, 2026	Identify CRISPR spacers in FASTA sequences and match them against viral databases	Defense Systems	github.com/ctSkennerton/minced	—
Prodigal	April 03, 2026	Translate nucleotide sequences into amino acid sequences using multi-fasta files	Sequences	github.com/hyattpd/prodigal	Hyatt et al. 2010
VIBRANT	April 3, 2026	Recover mobile genetic element sequences from metagenomes using metabolic HMM-based virome identification and annotation	Virus	github.com/AnantharamanLab/VIBRANT	Kieft et al. 2020
mTM-align	April 03, 2026	Multiple structure alignment (MSA) of protein structures	Protein Structure	yanglab.qd.sdu.edu.cn/mTM-align	Dong et al. 2018

Education

Navigate by experience level

Track 01

Foundations

Beginner

school

Lecture

Intro to Viral Ecology

Concepts of virus–host dynamics, ecological roles, and evolutionary significance.

3 h · Slides + Notes

terminal

Tutorial

Linux for Biologists

Command-line essentials for navigating, scripting, and running bioinformatics tools.

4 h · Self-paced

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Tutorial

Conda & Environments

Setting up reproducible software environments with Conda and Mamba.

1 h · Script Included

Track 02

Methods

Intermediate

groups

Workshop

Microbial Genomics Workshop

Assembly, annotation, and comparative analysis of archaeal and viral genomes.

2 days · Open Enrollment

manage_search

Tutorial

Virus Discovery 101

Step-by-step pipeline using VIBRANT and CheckV to identify viruses from metagenomes.

6 h · Dataset Included

code

Workshop

Bioinformatics Scripting

Python and R for automating data processing — no prior programming required.

8 h · 4 Modules

Track 03

Advanced

Expert

account_tree

Workshop

Phylogenomics & Evolution

Maximum-likelihood and Bayesian inference of viral and archaeal evolutionary trees.

1 day · IQ-TREE + BEAST

hub

Course

Pangenomics & MGE

Construction and analysis of pangenomes with focus on mobile genetic elements in archaea.

2 days · Research-grade

visibility

Tutorial

Advanced Microscopy

Techniques for super-resolution imaging of viral–host interactions at cellular resolution.

4 h · Lab Access Req.

Consulting & Training Services

We offer one-on-one consultations to understand your specific needs — whether you're looking to develop a custom bioinformatics pipeline or build hands-on skills in viral ecology and genomics. Get in touch to start the conversation.

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