PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
☆63May 5, 2026Updated 5 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 4 years ago
- Fast tool to build the core genome of prokaryotic genomes. Can handle large datasets. Dependencis: Usearch & Numpy☆10Nov 26, 2025Updated 10 months ago
- Metabolic scanning and annotation of Metagenomes☆10Dec 18, 2025Updated 9 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.
- A package to annotate protein sequences☆63Feb 23, 2025Updated last year
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆51Sep 4, 2026Updated last month
- post processing of bacterial pangenome gene presence/absence matrices☆68Jan 19, 2026Updated 8 months ago
- An updated pipeline for pangenome investigation☆375Jul 2, 2026Updated 3 months 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☆110Jun 25, 2023Updated 3 years ago
- A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.☆20Aug 7, 2026Updated 2 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Aug 8, 2022Updated 4 years ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- A viewer for multiple alignment format (MAF) files in JBrowse 2☆14Aug 4, 2026Updated 2 months ago
- 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.☆156Jul 24, 2026Updated 2 months ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆225Aug 27, 2025Updated last year
- Find and visualize rearrangements in DNA sequences☆56Jun 3, 2026Updated 4 months ago
- Bifrost graph gene caller.☆102Aug 31, 2026Updated last month
- Pooled Sequencing Analysis for Sex Signal☆15Sep 14, 2021Updated 5 years ago
- Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.☆15Apr 28, 2026Updated 5 months ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆72Aug 27, 2026Updated last month
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- 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☆23Apr 20, 2023Updated 3 years ago
- ⚡🦠🧬📇 Rapid microbial genomes-to-report pipeline☆75Sep 23, 2026Updated 2 weeks ago
- GEne Cluster prediction with COnditional random fields.☆90Jul 29, 2026Updated 2 months ago
- ☆13Sep 11, 2025Updated last year
- Wrapper for short and long read mapping, creation of quality report(s) and estimation of genome size☆12Sep 30, 2025Updated last year
- metagenome population recombination rate estimation pipeline☆12Nov 23, 2025Updated 10 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 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Gene cluster comparison figure generator☆655Updated this week
- A user-friendly workflow for phylogenomics☆234Sep 28, 2026Updated last week
- Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2☆80Aug 30, 2016Updated 10 years ago
- Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5☆101Mar 12, 2026Updated 6 months ago
- A genome completeness evaluation tool based on miniprot☆267Aug 17, 2026Updated last month
- ☆18Jun 5, 2026Updated 4 months ago
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆66Updated this week