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:
- Generate mutated sequence files from a reference genome.☆11Oct 14, 2026Updated 2 weeks ago
- 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 4 months ago
- THRESHER is a framework that replaces fixed cutoffs with data-driven phylothresholds - the SNP thresholds corrected for phylogenetic topo…☆14Oct 17, 2026Updated 2 weeks ago
- ☆16May 21, 2026Updated 5 months ago
- ☆10Jun 9, 2025Updated last year
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆226Oct 7, 2026Updated 3 weeks ago
- ARBitR: Assembly Refinement with Barcode-identity-tagged Reads☆10Oct 22, 2020Updated 6 years ago
- Resolving Species Level Classification Using Emu☆14Jun 14, 2024Updated 2 years ago
- Breakpointer is a fast algorithm to locate breakpoints of structural variants from single-end reads produced by next-generation sequencin…☆10May 2, 2014Updated 12 years ago
- RAPTR-SV uses Read Pair and Split Read methods to identify structural variants in paired-end WGS data☆10Aug 18, 2016Updated 10 years ago
- A high-performance in-silico PCR tool for primer matching and product extraction from FASTA and GenBank sequences.☆20Feb 25, 2026Updated 8 months ago
- 🚝RAILS and 👞🔨Cobbler: Assembly Improvement by Long Sequence Scaffolding/Gap-filling☆27Apr 1, 2026Updated 7 months ago
- Analyze a set of genomes with the anvi'o pangenome pipeline☆16Oct 11, 2023Updated 3 years ago
- ANNOgesic - A Swiss army knife for the RNA-Seq based annotation of bacterial/archaeal genomes☆34Feb 16, 2024Updated 2 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- skandiver is a program for identifying mobile genetic elements (prophages, plasmids, transposases, etc.) from assembled whole genome sequ…☆16Nov 20, 2025Updated 11 months ago
- Visualize microbial evolution at the SNP level!☆18Aug 12, 2025Updated last year
- Repository containing a method for automatically identifying pathogen lineages from a phylogeny.☆18May 19, 2023Updated 3 years ago
- Multisample Variant Format ToolKit☆10Oct 12, 2021Updated 5 years ago
- Fast C code for identifying and removing primers and adapters