The R package 'phylosamp' implements novel tools that estimate the probability of transmission between two cases given phylogenetic linkage and sample size calculations for phylogenetic studies.
☆14May 23, 2023Updated 3 years ago
Alternatives and similar repositories for phylosamp
Users that are interested in phylosamp 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.☆10Jun 9, 2026Updated 3 months ago
- ☆10Apr 16, 2025Updated last year
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆29Sep 3, 2026Updated 2 weeks ago
- UPHL's Reference Free Pipeline☆29Sep 4, 2026Updated 2 weeks ago
- LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations☆26Aug 26, 2024Updated 2 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- ☆21Apr 2, 2025Updated last year
- emm Automatic Isolate Labeller☆16Mar 25, 2025Updated last year
- ☆29May 19, 2026Updated 4 months ago
- Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.☆16Sep 8, 2026Updated 2 weeks ago
- Renders SVG schema of SARS-CoV-2 clade as defined by Nextstrain☆18Nov 24, 2025Updated 10 months ago
- Bacterial surveillance pipeline.☆30Updated this week
- Software for the Tree-Based Scan Statistic☆17Sep 15, 2026Updated last week
- MIRA: Portable, Interactive Application for High-Quality Influenza, SARS-CoV-2 and RSV Genome Assembly, Annotation, and Curation☆25Updated this week
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 3 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…☆43Aug 28, 2026Updated 3 weeks ago
- Consensus sequences for U.S. H5N1 clade 2.3.4.4b☆40Updated this week
- Miscellaneous helper tools for epidemiologists☆10Nov 9, 2025Updated 10 months ago
- ☆24Sep 3, 2026Updated 2 weeks ago
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 3 years ago
- An R package to help assess the sensitivity of a Bayesian model (fitted with Stan) to the specification of its likelihood and priors☆11May 29, 2026Updated 3 months ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆15Aug 26, 2024Updated 2 years ago
- MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates☆96Jul 23, 2026Updated 2 months ago
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆17Feb 19, 2026Updated 7 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- 🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens☆112Updated this week
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆57Jul 24, 2025Updated last year
- A curated database of completed assemblies with taxonomy IDs☆53Aug 31, 2026Updated 3 weeks ago
- ☆12Oct 11, 2022Updated 3 years ago
- The NCBI SARS-CoV-2 Variant Calling (SC2VC) Pipeline allows calling high-confidence variants from SARS-CoV-2 NGS data in a standardized f…☆14Apr 21, 2023Updated 3 years ago
- Lander Analytics Bayes/Stan Class 2021☆10Aug 3, 2021Updated 5 years ago
- Migrating from SAS to R☆16Feb 23, 2024Updated 2 years ago
- R package to run BEAST2☆11Dec 8, 2025Updated 9 months ago
- ☆20Apr 9, 2021Updated 5 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- de novo virus assembler of Illumina paired reads☆58May 17, 2021Updated 5 years ago
- Compile Stan models to WebAssembly.☆15May 14, 2023Updated 3 years ago
- Depth-weighted De-Mixing☆134Updated this week
- Survival modelling via ODEs☆11Aug 4, 2026Updated last month
- Shiny app providing estimates of future bed occupancy given recent admissions☆12Jul 2, 2020Updated 6 years ago
- Bayesian Modelling in Epidemiology Case Line Lists☆14Oct 7, 2025Updated 11 months ago
- Datasets for https://github.com/nextstrain/nextclade☆47Sep 15, 2026Updated last week