A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
☆60Dec 5, 2025Updated 4 months ago
Alternatives and similar repositories for get_phylomarkers
Users that are interested in get_phylomarkers are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- GET_HOMOLOGUES: a versatile software package for pan-genome analysis☆126Feb 13, 2026Updated 2 months ago
- Plot bacterial gene maps and genome comparison plots from command line with genoPlotR and GenomeDiagram☆13Mar 10, 2026Updated last month
- Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México☆26Oct 29, 2025Updated 5 months ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Apr 11, 2018Updated 8 years ago
- pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria☆11Feb 6, 2018Updated 8 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.
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆18Feb 12, 2016Updated 10 years ago
- IslandPath standalone software☆36Nov 7, 2023Updated 2 years ago
- Hybrid Assembler for Plasmids☆10Jul 28, 2022Updated 3 years ago
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆36Feb 3, 2021Updated 5 years ago
- hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance☆22Mar 8, 2024Updated 2 years ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆51Sep 23, 2022Updated 3 years ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 3 months ago
- R tools for reconstructing metabolisms.☆14Mar 10, 2026Updated last month
- Serverless GPU API endpoints on Runpod - Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- D3 based visualisation for comparative genomics☆15Oct 6, 2016Updated 9 years ago
- Download assembly files from NCBI☆13May 9, 2023Updated 2 years ago
- Automatically calculate phylogenetic trees from bacterial core genes☆20May 13, 2025Updated 11 months ago
- Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.☆121Jan 22, 2025Updated last year
- Bacterial taxonomy construction and evaluation in R☆16Jan 30, 2024Updated 2 years ago
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 2 years ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆121May 21, 2024Updated last year
- A toolkit for prokaryotic comparative genomics☆51Feb 23, 2026Updated last month
- Metabolic scanning and annotation of Metagenomes☆10Dec 18, 2025Updated 4 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Searching for Horizontal Gene Transfer☆10Feb 22, 2020Updated 6 years ago
- ISCompare, an opensource program to identify Differentially Located Insertion Sequences☆14Jul 30, 2024Updated last year
- Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method☆17Dec 29, 2022Updated 3 years ago
- Archived - please see updated sccmec tool at link below☆13Aug 30, 2024Updated last year
- Easy-to-use web application for visualization and comparison of genomes in Genbank file☆22May 27, 2022Updated 3 years ago
- The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline☆41Dec 8, 2022Updated 3 years ago
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆63Mar 3, 2026Updated last month
- Pan-genome wide association studies☆213May 29, 2024Updated last year
- IS mapping software☆57Dec 3, 2021Updated 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.
- Prokaryotic Pangenome Analysis☆24Dec 3, 2021Updated 4 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆32Apr 12, 2026Updated last week
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆13Jun 10, 2021Updated 4 years ago
- PANgenome with Annotations, COre identification, Tree and corresponding Alignments☆81Sep 20, 2023Updated 2 years ago
- In-depth characterization and annotation of differences between two sets of DNA sequences☆64May 18, 2020Updated 5 years ago
- Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations☆14Nov 24, 2025Updated 4 months ago
- Targeted Detection and Reconstruction of Plasmids☆22May 7, 2024Updated last year