a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
python bioinformatics genomics evolution phylogenetics phylogenomics evolutionary-biology systematics
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- Python
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evolutionary-biology
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a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
python bioinformatics genomics evolution phylogenetics phylogenomics evolutionary-biology multiple-sequence-alignments
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- Python
🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃♀️
bioinformatics r genomics bioconductor genes comparative-genomics r-package ontologies evolutionary-biology bioconductor-package translational-research animal-models biomedicine
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- R
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
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- Python
a broadly applicable tool for automated gene identification and retrieval
python bioinformatics genomics evolution phylogenetics orthology-inference phylogenomics evolutionary-biology orthology orthology-assignments
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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
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PyPop: Python for Population Genomics
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Create, modify and analyse phylogenetic trees in R
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Reproducible Quantitative Methods for EEB
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- TeX
a versatile toolkit for processing and analyzing diverse types of sequence data
python bioinformatics genomics evolution comparative-genomics evolutionary-biology evolutionary-genomics
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- Python
Evolutionary simulation where agents age, reproduce, and eat each other
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- C#
A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests and viral simulations at scale. Related manuscripts: https://doi.org/10.1111/2041-210X.14168 and https://doi.org/10.1038/s41467-025-60988-8
genome genetics anaconda cuda conda vcf epidemiology hiv viral-genomics 1000genomes evolutionary-biology neutrality ehh mk-test epidemic-simulations sars-cov-2 extended-haplotype-homozygosity tajima
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- Cuda
Computer vision benchmark for evolutionary biology-related tasks.
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- Python
Two-Tier Ensemble Aggregation Gene Co-expression Network (TEA-GCN): Capturing tissue/condition-specific co-expression from large transcriptomic datasets
transcriptomics evolutionary-biology gene-co-expression-network gene-functional-annotation gene-co-expression-network-analysis biological-network
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- Python
Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries
phylogenetics population-genetics paleobiology comparative-methods evolutionary-biology macroevolution science-education biodiversity-science simulation-based-learning inquiry-based-learning data-driven-education
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- R
HARE: Genetic Feature Enrichment Analysis Pipeline
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- Python
MSEABOARD: A web-based dashboard for interactive visualization and analysis of multiple sequence alignments, phylogenetic trees, protein structures, distance matrices and associated data.
react visualization javascript open-source bioinformatics dashboard structural-biology protein-structure computational-biology phylogenetic-trees phylogenetics evolutionary-biology multiple-sequence-alignment
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- JavaScript
Newick formatted (phylogenetic) trees
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- Julia
Software for analysing Many-Analysts' style data and generating the ManyEcoEvo project data
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- HTML
A Julia interface to the Paleobiology Database (PBDB) data service.
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- Julia
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