ML phylogenetic inference for non-model organisms with short reads & assemblies
☆15Jun 30, 2026Updated 2 months ago
Alternatives and similar repositories for orthogarden
Users that are interested in orthogarden are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- coevol -- Correlated evolution of substitution rates and quantitative traits☆13Oct 18, 2024Updated last year
- Visualing species tree from ASTRAL with gene tree discordance☆34Aug 21, 2026Updated last week
- Clade age estimation using a Bayesian Brownian bridge model☆15Sep 3, 2025Updated 11 months ago
- Modeling gene duplication, loss, and coalescence (through parsimony)☆10Jun 18, 2020Updated 6 years ago
- Tool for fully-automated inference of species trees from raw genome assemblies☆50Updated this week
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation☆16Apr 29, 2025Updated last year
- Robust identification of orthologous Synteny with the Orthology Index☆43Aug 22, 2026Updated last week
- convert variation graph alignments to coverage maps over nodes☆28Jan 21, 2026Updated 7 months ago
- phyloGAN is a Generative Adversarial Network (GAN) that infers phylognetic relationships.☆11Jul 8, 2024Updated 2 years ago
- A tool to root phylogenies☆23Sep 5, 2024Updated last year
- An R package to visualize chromosome scale repeat patterns and predict centromere locations.☆50May 8, 2026Updated 3 months ago
- Resistify is a program which rapidly identifies and classifies plant resistance genes from protein sequences. It is designed to be lightw…☆48Jul 22, 2026Updated last month
- Phyling: phylogenetic inference from annotated genomes☆32Jul 27, 2026Updated last month
- ARCHIVED Access sequences from the 1000 Plant Initiative (1KP)☆13Nov 7, 2025Updated 9 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Transposable element expression at unique loci in single cells with CELLO-seq☆12Jun 17, 2024Updated 2 years ago
- An Example of Subgenome Phasing for Complex Allopolyploidy☆17Nov 6, 2025Updated 9 months ago
- R package for simulating fossil data on phylogenetic trees under mechanistic models of preservation and sampling☆12Jun 3, 2026Updated 2 months ago
- A pipeline for the analysis of sedimentary ancient mtDNA.☆18Updated this week
- ☆49Sep 5, 2023Updated 2 years ago
- MCMCtreeR: A package to estimate distribution values for temporal node constraints and prepare input files for MCMCtree☆46Nov 21, 2019Updated 6 years ago
- Associated code for EvoWeaver publication☆17May 19, 2025Updated last year
- CPANG19 - Computational PANGenomics (2019)☆12May 7, 2020Updated 6 years ago
- Rapid estimation of phylogenetic trees using sketching☆13Feb 18, 2025Updated last year
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Galaxy Docker Image with Tools for Genome Annotation☆12Apr 20, 2021Updated 5 years ago
- ☆17Mar 7, 2025Updated last year
- COsine SImilarity-based Genotyper using pangenomes☆36Aug 18, 2026Updated last week
- a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies☆89Aug 19, 2026Updated last week
- Efficient indexing and querying of annotations in a pangenome graph☆10Oct 29, 2025Updated 10 months ago
- Quality assessment of de novo transcriptome assemblies from RNA-Seq data☆26Nov 14, 2025Updated 9 months ago
- A program to generate a graph which presents a simplified representation of several full length genomes☆13Aug 23, 2018Updated 8 years ago
- Infering ancestral synteny with hierarchical orthologous groups☆38Jun 26, 2026Updated 2 months ago
- Estimate node ages of a phylogeny by approximating the phylogenetic likelihood with a multivariate normal distribution.☆12Jun 23, 2025Updated last year
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Python library for accessing Kew's data services☆36Jan 25, 2022Updated 4 years ago
- Statistics and analysis for variation graphs☆53Dec 17, 2024Updated last year
- generalized linear/mixed models workshop, Morelia 2018☆14Jul 26, 2022Updated 4 years ago
- PG-SCUnK mesure quality of Pan-Genome Graphs using Single Copy and Universal k-mers☆25Feb 16, 2026Updated 6 months ago
- ANI based satellite annotation☆29Aug 6, 2026Updated 3 weeks ago
- ☆19May 10, 2023Updated 3 years ago
- Population genetics analysis on VG☆17Apr 22, 2021Updated 5 years ago