PyPop: Python for Population Genomics
-
Updated
Oct 22, 2025 - Python
#
evolutionary-biology
Here are 22 public repositories matching this topic...
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
python bioinformatics genomics evolution phylogenetics phylogenomics evolutionary-biology systematics
-
Updated
Oct 17, 2025 - Python
Computer vision model to detect drosophila eggs from full caps using a novel technique called "Tiling"
-
Updated
Oct 4, 2025 - Python
This repository contains Python and NetLogo simulations based on the paper "The conditional defector strategies can violate the most crucial supporting mechanisms of cooperation" (Scientific Reports, 2022). The models explore evolution of cooperation, conditional defection, and mechanisms like kin selection, spatial structure, and punishment.
python matplotlib agent-based-modeling netlogo evolutionary-computation evolutionary-strategy ecological-modelling agent-based-simulation evolutionary-biology evolutionary-game-theory adaptive-dynamics evolutionary-dynamics
-
Updated
Oct 2, 2025 - Python
Supporting code for a study on the phylogeography of the common gartersnake (Thamnophis sirtalis)
geospatial-data phylogeography population-genetics evolutionary-biology herpetology ecological-niche-modeling demographic-modeling rangemaps
-
Updated
Oct 1, 2025 - Python
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
python bioinformatics genomics evolution phylogenetics phylogenomics evolutionary-biology multiple-sequence-alignments
-
Updated
Sep 25, 2025 - Python
a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
python bioinformatics genomics evolution phylogenetics orthology-inference phylogenomics evolutionary-biology orthology orthology-assignments
-
Updated
Sep 16, 2025 - Python
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
bioinformatics supermatrix phylogenetics comparative-genomics comparative-genomics-studies phylogeny whole-genome-sequencing whole-genome evolutionary-biology concatination bacterial-genomics
-
Updated
Sep 5, 2025 - Python
A workflow to simulate selective sweeps in SLiM and turn the results into images
-
Updated
Jul 20, 2025 - Python
Repo for the biological analyses performed on taxonomic quasi-prime peptides.
-
Updated
Jul 12, 2025 - Python
Numerical model for life history evolution of age-structured populations
-
Updated
Jun 18, 2025 - 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.
-
Updated
Apr 2, 2025 - Python
The graph-based fitness landscape analysis framework
-
Updated
Jan 10, 2025 - Python
Experiments with the BEAST 2 software
phylogenetic-trees phylogenetics bayesian phylogeography bayesian-inference bayesian-statistics phylogeny evolutionary phylodynamics beast2 evolutionary-biology compartmental-models compartmental-model evolutionary-models compartmental-modeling
-
Updated
Jan 9, 2025 - Python
a versatile toolkit for processing and analyzing diverse types of sequence data
python bioinformatics genomics evolution comparative-genomics evolutionary-biology evolutionary-genomics
-
Updated
Dec 6, 2024 - Python
a broadly applicable tool for automated gene identification and retrieval
python bioinformatics genomics evolution phylogenetics orthology-inference phylogenomics evolutionary-biology orthology orthology-assignments
-
Updated
Dec 6, 2024 - Python
HARE: Genetic Feature Enrichment Analysis Pipeline
-
Updated
May 28, 2024 - Python
HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.
systems-biology phylogenetics horizontal-gene-transfer sequence-analysis evolutionary-biology high-throughput-pipeline
-
Updated
Feb 11, 2023 - Python
-
Updated
Dec 19, 2022 - Python
Simulating evolution of behavioral traits with Python
behavior simulation biology evolution evolutionary-algorithms simulations survival reproduction evolutionary-algorithm natural-selection evolutionary-biology altruistic-individuals behavioral-traits
-
Updated
Apr 22, 2022 - Python
Improve this page
Add a description, image, and links to the evolutionary-biology topic page so that developers can more easily learn about it.
Add this topic to your repo
To associate your repository with the evolutionary-biology topic, visit your repo's landing page and select "manage topics."