iferres / pagooLinks
A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.
☆28Updated 2 years ago
Alternatives and similar repositories for pagoo
Users that are interested in pagoo are comparing it to the libraries listed below
Sorting:
- Bacterial GWAS analysis☆46Updated 2 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆32Updated last month
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆39Updated 3 months ago
- Calculate assocations between genes and traits☆29Updated 10 months ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆62Updated 2 years ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Updated 3 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Updated 3 years ago
- Discover and annotate the virome☆58Updated 2 months ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Updated 3 years ago
- Gene-flank analysis tool☆34Updated last year
- ☆13Updated 8 years ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated 2 years ago
- BEAV: Bacterial Element Annotation reVamped☆73Updated 4 months ago
- Phylogeny Enhanded Prediction of PAN-genome☆43Updated 5 years ago
- A taxonomic classifier of plasmids☆28Updated 4 years ago
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆15Updated 3 years ago
- Genomewide Epistasis Analysis on Bacteria☆15Updated 7 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated 8 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆25Updated last year
- Automated strain separation of low-complexity metagenomes☆52Updated 4 years ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆68Updated 3 years ago
- MAG Circularization Method☆32Updated 2 months ago
- ☆24Updated 11 months ago
- A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concat…☆59Updated last month
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆27Updated last month
- Gene tree - species tree reconciliation from gene tree distributions☆37Updated last month
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 6 months ago
- Inferring global and local strict molecular clocks using root-to-tip regression☆14Updated last month
- EzAAI - High Throughput Prokaryotic AAI Calculator☆45Updated 5 months ago