xavierdidelot / ClonalFrameML
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
☆108Updated 6 months ago
Related projects ⓘ
Alternatives and complementary repositories for ClonalFrameML
- phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.☆77Updated last year
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆107Updated last week
- GET_HOMOLOGUES: a versatile software package for pan-genome analysis☆110Updated last week
- Massively parallel phylogenetic placement of genetic sequences☆78Updated 2 years ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆127Updated 8 months ago
- Making whole bacterial genome sequencing data analysis easy☆99Updated last week
- A toolbox for comparative genomics.☆97Updated 3 years ago
- A tool for the identification of coincident (associating and dissociating) genes in pangenomes.☆97Updated last year
- SKESA assembler☆112Updated last month
- A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework☆78Updated 5 months ago
- Create a tree using Mash distances☆156Updated last year
- A toolbox for pangenome analysis and threshold evaluation.☆91Updated 2 years ago
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆110Updated last year
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆83Updated last month
- Metagenomic classification of long-read sequencing data☆61Updated this week
- Pan-genome wide association studies☆150Updated 5 months ago
- ☆116Updated this week
- Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data☆109Updated last year
- Synteny Imager☆60Updated 2 months ago
- Collection of scripts for bacterial genomics☆44Updated 4 years ago
- IS mapping software☆51Updated 2 years ago
- Foreign Contamination Screening caller scripts and documentation☆106Updated this week
- BSR-Based Allele Calling Algorithm☆134Updated 2 weeks ago
- ☆68Updated 10 months ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆71Updated 3 months ago
- r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)☆63Updated 11 months ago
- Recentrifuge: robust comparative analysis and contamination removal for metagenomics☆86Updated last month
- DDBJ Fast Annotation and Submission Tool☆78Updated last month
- ☆79Updated last year
- a collection of scripts for organising bacterial genomes by species☆76Updated 2 years ago