Reconstruction of transmission trees using genomic data
☆72Sep 27, 2023Updated 2 years ago
Alternatives and similar repositories for TransPhylo
Users that are interested in TransPhylo are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Disease outbreak reconstruction from epidemiological and genetic data☆35Mar 27, 2026Updated 2 weeks ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆97Dec 9, 2025Updated 4 months ago
- Pipeline to generate NGS reads from a phylogeny☆39Sep 13, 2022Updated 3 years ago
- pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria☆11Feb 6, 2018Updated 8 years ago
- Infer transmission clusters from SNP and timing data☆16May 20, 2020Updated 5 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆121May 21, 2024Updated last year
- Algorithm to divide a phylogenetic tree into segments based on phenotypes at the leaves of the tree☆25Jul 13, 2018Updated 7 years ago
- baltic - adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. This fork will no longe…☆12Dec 18, 2019Updated 6 years ago
- Whole genome core alignments from multiple draft genomes☆13Sep 14, 2016Updated 9 years ago
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆251Updated this week
- Analysis of global migration patterns of seasonal influenza viruses☆22Jul 24, 2019Updated 6 years ago
- treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes☆106Feb 6, 2025Updated last year
- Scalable relaxed clock phylogenetic dating☆28Sep 3, 2025Updated 7 months ago
- Finding prophage regions in bacterial genomes using brute force☆22Jan 20, 2023Updated 3 years ago
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Phylogenetics between and within hosts at once, all along the genome.☆51Oct 2, 2024Updated last year
- SaffronTree: Reference free rapid phylogenetic tree construction from raw read data☆25Jun 11, 2020Updated 5 years ago
- Cluster Investigation & Virus Epidemiology Tool☆50Jun 17, 2025Updated 9 months ago
- Rapid haploid variant calling and core genome alignment☆576Dec 12, 2025Updated 4 months ago
- Inferring spatiotemporal dynamics of the H1N1 influenza pandemic from sequence data☆33Oct 25, 2013Updated 12 years ago
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆14Jun 12, 2024Updated last year
- PLSDB pipeline to collect bacterial plasmids from NCBI☆40Oct 23, 2024Updated last year
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated last month
- ☆12Feb 9, 2025Updated last year
- Deploy open-source AI quickly and easily - Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development…☆117Apr 3, 2026Updated last week
- Pairwise SNP distance matrix from a FASTA sequence alignment☆153Dec 31, 2025Updated 3 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆48Feb 20, 2026Updated last month
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆29Feb 12, 2026Updated 2 months ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆216Aug 27, 2025Updated 7 months ago
- A list of weak Bacterial assemblies in GenBank☆18Aug 3, 2017Updated 8 years ago
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- Fast genealogical relationship evaluation of bacterial isolates with WGS data.☆12Jan 17, 2022Updated 4 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- A snakemake workflow for WGS-based tuberculosis transmission analysis☆20Dec 3, 2024Updated last year
- GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click…☆87Dec 15, 2024Updated last year
- Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment☆16Dec 5, 2018Updated 7 years ago
- REcombination BARcode detector.☆16Apr 2, 2024Updated 2 years ago
- Northern Arizona SNP Pipeline☆20Oct 29, 2024Updated last year
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆29Mar 10, 2026Updated last month
- Ultrafast Sample Placement on Existing Trees☆140Feb 6, 2026Updated 2 months ago