irycisBioinfo / PATOLinks
PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
☆62Updated 2 years ago
Alternatives and similar repositories for PATO
Users that are interested in PATO are comparing it to the libraries listed below
Sorting:
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆46Updated 2 years ago
- Bacterial GWAS analysis☆46Updated 2 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆32Updated 3 weeks ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆69Updated 4 years ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆45Updated 4 months ago
- BEAV: Bacterial Element Annotation reVamped☆72Updated 4 months ago
- A toolkit for prokaryotic comparative genomics☆51Updated 2 months ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆70Updated this week
- ☆54Updated 5 months ago
- The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline☆41Updated 3 years ago
- IslandPath standalone software☆34Updated 2 years ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆35Updated 2 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆43Updated 5 years ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50Updated last year
- Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.☆27Updated 8 months ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆36Updated 4 years ago
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆22Updated 2 years ago
- A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concat…☆59Updated 3 weeks ago
- Gene-flank analysis tool☆34Updated last year
- Ley Lab MetaGenome Profiler DataBase generator☆50Updated 3 years ago
- Microbial Populations as Clusters Of Gene Transfer☆45Updated 2 years ago
- GTDB taxonomy taxdump files with trackable TaxIds☆56Updated 7 months ago
- A tool for removing redundant genomes from a set of assemblies☆77Updated 3 months ago
- whole genome MLST analysis☆50Updated 6 months ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆49Updated 2 years ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated 2 years ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated 8 months ago
- ☆33Updated 2 years ago
- MetaGeneMark-2: Improved Gene Prediction in Metagenomes☆22Updated last year