BDI-pathogens / phyloscannerLinks
Phylogenetics between and within hosts at once, all along the genome.
☆50Updated 11 months ago
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☆49Updated 2 years ago
- Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.☆48Updated 3 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- Reconstruction of transmission trees using genomic data☆63Updated last year
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- De novo Extraction of Strains from MetAgeNomes☆71Updated 5 years ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆66Updated 3 years ago
- Pipeline to generate NGS reads from a phylogeny☆39Updated 3 years ago
- A set of scripts for calculating pairwise SNP distance☆42Updated 2 years ago
- Recombination-free trees☆60Updated 3 weeks ago
- A resistome profiler for Graphing Resistance Out Of meTagenomes☆66Updated 5 years ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 6 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆56Updated 4 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- Visualize whole genome alignments as linear maps☆73Updated last month
- Gene-flank analysis tool☆30Updated 9 months ago
- ☆36Updated 5 months ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆91Updated last month
- ☆53Updated 4 years ago
- GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click…☆83Updated 9 months ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆29Updated last year
- scripts for estimating bacteria replication rates based on population genome copy number variation☆72Updated 5 years ago
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆29Updated last year
- a collection of scripts for organising bacterial genomes by species☆76Updated 3 years ago
- BEAV: Bacterial Element Annotation reVamped☆68Updated last month
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆39Updated 5 months ago
- Cluster Investigation & Virus Epidemiology Tool☆50Updated 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