Virus reassortment inference software. Infers both recent and ancestral reassortment and uses flexible molecular clock constraints.
☆23Sep 29, 2025Updated 8 months ago
Alternatives and similar repositories for TreeSort
Users that are interested in TreeSort are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10May 15, 2026Updated 3 weeks ago
- Consensus sequences for U.S. H5N1 clade 2.3.4.4b☆37Updated this week
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆41Mar 31, 2026Updated 2 months ago
- R package for studying phylogenetically-informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al. 2026, Bioinformatics)☆43Mar 24, 2026Updated 2 months ago
- Main development repository for SpreadGL☆22Sep 30, 2024Updated last year
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Simple Manipulation Of Trees☆14Aug 16, 2025Updated 9 months ago
- A forward-time simulator for gene sequences modeling a variety of mutation and selection processes.☆21Aug 23, 2023Updated 2 years ago
- Visualization tool for genetic reassortment☆21Apr 29, 2026Updated last month
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19May 3, 2024Updated 2 years ago
- A multi-algorithmic framework for phylogenetic inference☆14Nov 28, 2025Updated 6 months ago
- Influenza data pipeline to automate genotyping assignment☆42Mar 19, 2026Updated 2 months ago
- Java software to analyse phylogeny-trait correlations in discrete traits, accounting for phylogenetic uncertainty via posterior sampling.☆13Sep 26, 2017Updated 8 years ago
- Inference framework for serological data☆20Mar 31, 2026Updated 2 months ago
- FluMut is a command-line tool to find markers of interest in H5N1 avian influenza viruses.☆15Updated this week
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Repository containing a method for automatically identifying pathogen lineages from a phylogeny.☆17May 19, 2023Updated 3 years ago
- Hybridization probe design for targeted genomic sequencing of diverse and hypervariable viral taxa☆25May 30, 2023Updated 3 years ago
- Munge GenBank files into FASTA and tab-separated metadata☆15Feb 5, 2026Updated 4 months ago
- A collection of documented examples using TreeTime☆22Jul 30, 2019Updated 6 years ago
- Influenza genome analysis Nextflow workflow☆32Sep 15, 2025Updated 8 months ago
- Fast viral consensus genome reconstruction☆27Feb 5, 2026Updated 4 months ago
- A protein language model for learning the SARS-CoV-2 fitness landscape☆13Apr 22, 2025Updated last year
- Material for the lecture Statistical Computing☆12Jan 1, 2026Updated 5 months ago
- Racmacs R package for performing antigenic cartography☆24Jun 27, 2024Updated last year
- 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.
- Prediction fitness of leaves on a genealogical tree☆12May 7, 2015Updated 11 years ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆40Apr 6, 2026Updated 2 months ago
- Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates☆21Nov 8, 2024Updated last year
- Welcome to the StrainHub Repo - Files and Data - StrainHub Online:☆18Jun 26, 2022Updated 3 years ago
- Processing and analysis of data coming from Illumina sequencing machines☆10Apr 16, 2026Updated last month
- Scripts, HMMs and search databases for identifying and classifying viral RdRp sequences☆14May 17, 2026Updated 3 weeks ago
- Fast inference for Generalised Linear Mixed Models.☆14Jan 17, 2025Updated last year
- Bioinformatics Training Platform (BTP) Workshop: Introduction to NGS☆10Oct 31, 2018Updated 7 years ago
- This is a deep learning method for identification of viral contigs with short length from metagenomic data.☆10Dec 20, 2021Updated 4 years ago
- 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.
- Epidemiological modeling framework for pathogen population genetics and evolution.☆19Oct 7, 2024Updated last year
- Miscellaneous helper tools for epidemiologists☆10Nov 9, 2025Updated 7 months ago
- Utilities and distributions for (birth-death) skyline models.☆10Aug 27, 2019Updated 6 years ago
- ☆30Mar 6, 2025Updated last year
- Scripts. config, and snakefiles for seasonal-flu nextstrain builds☆62May 25, 2026Updated 2 weeks ago
- ☆15Oct 7, 2025Updated 8 months ago
- Rapid analysis and visualization of coronavirus genome variation☆48Apr 2, 2026Updated 2 months ago