Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.
☆34Nov 28, 2023Updated 2 years ago
Alternatives and similar repositories for PhaME
Users that are interested in PhaME are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organism…☆67Jun 11, 2026Updated 2 months ago
- Generate mutated sequence files from a reference genome.☆11Jun 12, 2026Updated 2 months ago
- ☆16May 21, 2026Updated 2 months ago
- ☆10Jun 9, 2025Updated last year
- Visualize microbial evolution at the SNP level!☆16Aug 12, 2025Updated last year
- 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.
- skandiver is a program for identifying mobile genetic elements (prophages, plasmids, transposases, etc.) from assembled whole genome sequ…☆15Nov 20, 2025Updated 8 months ago
- ANNOgesic - A Swiss army knife for the RNA-Seq based annotation of bacterial/archaeal genomes☆34Feb 16, 2024Updated 2 years ago
- Analyze a set of genomes with the anvi'o pangenome pipeline☆16Oct 11, 2023Updated 2 years ago
- Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.☆11Jul 30, 2026Updated last week
- A taxonomic classifier of plasmids☆29Jul 7, 2021Updated 5 years ago
- Multisample Variant Format ToolKit☆10Oct 12, 2021Updated 4 years ago
- Whole genome focused array SNP typer☆14Feb 2, 2026Updated 6 months ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆221Aug 27, 2025Updated 11 months ago
- VIGOR4☆23Aug 15, 2025Updated 11 months 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.
- INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search☆15Dec 14, 2022Updated 3 years ago
- ☆16Jan 28, 2026Updated 6 months ago
- NaS is a hybrid approach developped to take advantage of data generated using MinION device. We combine Illumina and Oxford Nanopore tech…☆15Mar 28, 2017Updated 9 years ago
- CroCoDeEL detects cross-sample contamination in shotgun metagenomic data☆32Jun 12, 2026Updated 2 months ago
- Scripts to analyze gene content and make a concatenated alignment of core genes from bacterial genomes.☆19Jul 20, 2018Updated 8 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- Taxonomic Classification of Bacteria and Archaea Genomes☆19May 20, 2026Updated 2 months ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- A pipeline for the computational evaluation of RNA-Seq data☆40Sep 10, 2024Updated last year
- 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.
- A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineere…☆20Aug 3, 2026Updated last week
- Short Read Sequence Typing for Bacterial Pathogens☆150Jun 20, 2021Updated 5 years ago
- Code for the Brassica oleracea/rapa/napus genomic comparison☆16Apr 29, 2021Updated 5 years ago
- PanEffect is a JavaScript framework to explore variant effects across a pangenome. The tool has two views that allows a user to (1) expl…☆13Jan 30, 2024Updated 2 years ago
- ☆18Jul 27, 2023Updated 3 years ago
- A simple script to run an alignment with nucmer and visualise its results.☆10Apr 17, 2023Updated 3 years ago
- ☆49Mar 19, 2023Updated 3 years ago
- This repository contains the reference genome assembly Ash1, built from data collected from an Ashkenazi individual.☆12Feb 2, 2022Updated 4 years ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆28Feb 12, 2026Updated 6 months ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Reference-guided multiple sequence alignment of viral genomes☆73May 30, 2026Updated 2 months ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆28Feb 6, 2023Updated 3 years ago
- ☆13Sep 11, 2025Updated 11 months ago
- Synteny and Rearrangement Identifier☆482Jul 1, 2026Updated last month
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆38Jun 4, 2026Updated 2 months ago
- Repository containing a method for automatically identifying pathogen lineages from a phylogeny.☆17May 19, 2023Updated 3 years ago
- IS mapping software☆59Dec 3, 2021Updated 4 years ago