PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
☆63May 5, 2026Updated 2 months ago
Alternatives and similar repositories for PATO
Users that are interested in PATO 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 comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.☆28Feb 14, 2023Updated 3 years ago
- A tool for the identification of coincident (associating and dissociating) genes in pangenomes.☆112Oct 20, 2023Updated 2 years ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆51Sep 23, 2022Updated 3 years ago
- Fast tool to build the core genome of prokaryotic genomes. Can handle large datasets. Dependencis: Usearch & Numpy☆10Nov 26, 2025Updated 7 months ago
- Metabolic scanning and annotation of Metagenomes☆10Dec 18, 2025Updated 7 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.
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50May 18, 2026Updated 2 months ago
- A package to annotate protein sequences☆63Feb 23, 2025Updated last year
- post processing of bacterial pangenome gene presence/absence matrices☆67Jan 19, 2026Updated 6 months ago
- An updated pipeline for pangenome investigation☆365Jul 2, 2026Updated 2 weeks ago
- R package for microbial pangenomics☆25Apr 12, 2022Updated 4 years ago
- hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance☆23Mar 8, 2024Updated 2 years ago
- GenoVi, an automated customizable circular genome visualizer for bacteria and archaea☆108Jun 25, 2023Updated 3 years ago
- A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.☆18Apr 4, 2026Updated 3 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Aug 8, 2022Updated 3 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- A viewer for multiple alignment format (MAF) files in JBrowse 2☆14Jun 3, 2026Updated last month
- Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments☆109Dec 11, 2023Updated 2 years ago
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆151Jul 4, 2026Updated 2 weeks ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆221Aug 27, 2025Updated 10 months ago
- Find and visualize rearrangements in DNA sequences☆55Jun 3, 2026Updated last month
- Pooled Sequencing Analysis for Sex Signal☆15Sep 14, 2021Updated 4 years ago
- Bifrost graph gene caller.☆98Jun 18, 2026Updated last month
- Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.☆14Apr 28, 2026Updated 2 months ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆72Updated this week
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Program for finding horizontal gene transfer using BLAST result☆11May 26, 2023Updated 3 years ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆22Apr 20, 2023Updated 3 years ago
- 🦠🧬🧑💻📇 Microbial genomes-to-report pipeline☆75Mar 14, 2026Updated 4 months ago
- GEne Cluster prediction with COnditional random fields.☆85Mar 10, 2026Updated 4 months ago
- ☆13Sep 11, 2025Updated 10 months ago
- Wrapper for short and long read mapping, creation of quality report(s) and estimation of genome size☆12Sep 30, 2025Updated 9 months ago
- metagenome population recombination rate estimation pipeline☆12Nov 23, 2025Updated 7 months ago
- Predict the function of phage hypothetical proteins using an LSTM model trained with Phage Synteny☆61Jun 4, 2025Updated last year
- Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin☆15Sep 24, 2024Updated last year
- 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.
- Gene cluster comparison figure generator☆648Dec 22, 2025Updated 7 months ago
- A user-friendly workflow for phylogenomics☆231Updated this week
- Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2☆79Aug 30, 2016Updated 9 years ago
- A genome completeness evaluation tool based on miniprot☆254Updated this week
- ☆17Jun 5, 2026Updated last month
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆67Apr 30, 2026Updated 2 months ago
- Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5☆90Mar 12, 2026Updated 4 months ago