HyPhy: Hypothesis testing using Phylogenies
☆264Jun 4, 2026Updated last week
Alternatives and similar repositories for hyphy
Users that are interested in hyphy are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Request execution of Galaxy SARS-CoV-2 variation analysis workflows on input data you provide.☆20Dec 13, 2021Updated 4 years ago
- Collection of scripts for automated SARS-CoV-2 genome surveillance.☆24Sep 19, 2023Updated 2 years ago
- ENA upload cli - script your Open Data upload to the European Nucleotide Archive☆29May 11, 2026Updated last month
- HyPhy standalone analyses☆54Jan 5, 2026Updated 5 months ago
- PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **techni…☆197Jan 29, 2026Updated 4 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Methods for finding associations between phenotypic and genomic differences between species using the Forward Genomics framework☆24Mar 26, 2026Updated 2 months ago
- Version 5 of the CAFE phylogenetics software☆170Mar 16, 2026Updated 2 months ago
- Estimating gene family turnover rates by likelihood-based methods☆12Aug 17, 2020Updated 5 years ago
- Phylogenetic orthology inference for comparative genomics☆858Jul 15, 2025Updated 10 months ago
- TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…☆207Nov 23, 2025Updated 6 months ago
- Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures☆126Feb 3, 2023Updated 3 years ago
- HyPhy tutorials☆11Apr 9, 2018Updated 8 years ago
- BITACORA: A Bioinformatics tool for gene family annotation☆54Dec 10, 2025Updated 6 months ago
- SyntenyFinder contains a collection of scripts for performing and visualizing macrosynteny analyses. It supports annotated chromosome-lev…☆35Jan 15, 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.
- Analysis of convergence between organismal traits and DNA/protein sequences☆66Apr 17, 2026Updated last month
- Newick tree processing☆13May 27, 2026Updated 2 weeks ago
- ☆81May 2, 2026Updated last month
- PhyloAcc a software to detect the changes of conservation of a genomic region☆36May 11, 2026Updated last month
- Convergent substitution detection tool based on the PCOC model☆31Dec 2, 2021Updated 4 years ago
- A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0☆262Updated this week
- PhyloBayes: phylogenetic reconstruction using infinite mixtures (CAT and CAT-GTR) -- serial version (for MPI, see pbmpi.git)☆15Oct 21, 2021Updated 4 years ago
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆252Updated this week
- Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)☆248Jun 5, 2026Updated last week
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies☆86Jun 4, 2026Updated last week
- Gene tree - species tree reconciliation from gene tree distributions☆41Apr 30, 2026Updated last month
- Analyzing combinations of codon substitution histories☆47Jun 3, 2026Updated last week
- Genome wide orthology inference and dNdS estimation☆101Jun 4, 2026Updated last week
- Python HyPhy: Facilitating HyPhy execution and parsing☆21Dec 7, 2021Updated 4 years ago
- ☆348Mar 4, 2025Updated last year
- RAxML Next Generation: faster, easier-to-use and more flexible☆466Updated this week
- Scalable relaxed clock phylogenetic dating☆27Sep 3, 2025Updated 9 months ago
- Clann: Investigation of phylogenomic signal using supertrees☆18Apr 21, 2026Updated last month
- 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.
- Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/☆572May 18, 2026Updated 3 weeks ago
- Killifish genomics scripts☆12Feb 19, 2021Updated 5 years ago
- Scripts used in the annotation of B10K genomes☆16Jun 1, 2020Updated 6 years ago
- An imagemagick-like frontend to Biopython SeqIO☆118Mar 18, 2024Updated 2 years ago
- shell tools for processing phylogenetic trees☆119Aug 30, 2022Updated 3 years ago
- Best-fit model selection☆89Mar 21, 2024Updated 2 years ago
- Tools for improving the sensitivity and specificity of genome alignments☆58Mar 12, 2026Updated 3 months ago