BDI-pathogens / phyloscannerLinks
Phylogenetics between and within hosts at once, all along the genome.
☆50Updated last year
Alternatives and similar repositories for phyloscanner
Users that are interested in phyloscanner are comparing it to the libraries listed below
Sorting:
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Updated 3 years ago
- Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.☆50Updated 3 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆68Updated 3 years ago
- Pipeline to generate NGS reads from a phylogeny☆39Updated 3 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- A set of scripts for calculating pairwise SNP distance☆43Updated 2 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- Cluster Investigation & Virus Epidemiology Tool☆50Updated 5 months ago
- Recombination-free trees☆60Updated 2 months ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆58Updated last month
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆31Updated last year
- De novo Extraction of Strains from MetAgeNomes☆71Updated 5 years ago
- Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2☆76Updated 9 years ago
- Surveillance of pathogens using population genomics and sequencing☆52Updated last month
- ☆36Updated 7 months ago
- A resistome profiler for Graphing Resistance Out Of meTagenomes☆65Updated 5 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆42Updated last month
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆92Updated 3 months ago
- This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…☆58Updated 4 years ago
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆45Updated 5 years ago
- Gene-flank analysis tool☆33Updated 11 months ago
- Ley Lab MetaGenome Profiler DataBase generator☆49Updated 3 years ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆56Updated 4 years ago
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- Rapid and scalable homolog identification for bacterial genomes☆33Updated 6 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 6 years ago
- a collection of scripts for organising bacterial genomes by species☆81Updated 3 years ago