a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

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

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

a broadly applicable tool for automated gene identification and retrieval

a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

PyPop: Python for Population Genomics

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

HARE: Genetic Feature Enrichment Analysis Pipeline

Numerical model for life history evolution of age-structured populations

Repo for the biological analyses performed on taxonomic quasi-prime peptides.

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

Computer vision model to detect drosophila eggs from full caps using a novel technique called "Tiling"

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

This repository provides an easy-to-use Python-based pipeline for reconstructing phylogenetic trees from whole bacterial genomes. It automates the process of identifying orthologous single-copy genes, aligning sequences, trimming alignments, and generating a concatenated supermatrix ready for phylogenetic analysis. The pipeline requires only .fasta

Experiments with the BEAST 2 software

The graph-based fitness landscape analysis framework

A workflow to simulate selective sweeps in SLiM and turn the results into images

Simulating evolution of behavioral traits with Python

Files pertaining to the processing of NGS data in .fasta.gz format for the purposes of identifying the genomic sequences which belong to either of the tuataras dual mitochondrial genomes.

Supporting code for a study on the phylogeography of the common gartersnake (Thamnophis sirtalis)