Reproducible Quantitative Methods for EEB

PyPop: Python for Population Genomics

a versatile toolkit for processing and analyzing diverse types of sequence data

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

Create, modify and analyse phylogenetic trees in R

Evolutionary simulation where agents age, reproduce, and eat each other

HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃‍♀️

R package: BALCONY (Better ALignment CONsensus analYsis)

Newick formatted (phylogenetic) trees

Numerical model for life history evolution of age-structured populations

Evolutionary genomics of chromosomal inversions in Atlantic herring

Bio-ModelChecker: Using Bounded Constraint Satisfaction to Seamlessly Integrate Observed Behavior with Prior Knowledge of Biological Networks

Two-Tier Ensemble Aggregation Gene Co-expression Network (TEA-GCN): Capturing tissue/condition-specific co-expression from large transcriptomic datasets

Source code for ManyEcoEvo Manuscript

A simple python3 program to compare aligned DNA/protein sequences.

HARE: Genetic Feature Enrichment Analysis Pipeline

R codes for simulating and detecting punctuated evolution in any clades, from dinosaurs to viruses

MSEABOARD: An open-source, web-based dashboard for interactive visualization and analysis of multiple sequence alignments, phylogenetic trees, protein structures, distance matrices and associated data.