santeripuranen / SpydrPick
SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.
☆13Updated 2 years ago
Alternatives and similar repositories for SpydrPick:
Users that are interested in SpydrPick are comparing it to the libraries listed below
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆18Updated 2 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- Plasmid analysis using rearrangement distances☆31Updated 2 months ago
- Recombination-free trees☆56Updated last year
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆36Updated last year
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆22Updated 5 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆25Updated 2 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆48Updated 6 months ago
- Bacterial GWAS analysis☆34Updated last month
- Calculate assocations between genes and traits☆20Updated 2 months ago
- Genomewide Epistasis Analysis on Bacteria☆14Updated 4 months ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆46Updated 2 years ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated last year
- A pipeline for performing genome-wide association tests for bacterial genomes.☆28Updated 6 years ago
- IslandPath standalone software☆31Updated last year
- Gene-flank analysis tool☆26Updated last month
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆41Updated 3 weeks ago
- Detect contigs of complete circular genomes☆22Updated 5 years ago
- strain-level analysis tools☆33Updated 2 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 5 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆19Updated 3 months ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆25Updated 2 months ago
- Genome size estimation from long read overlaps☆47Updated last month
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆28Updated 6 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆41Updated last month
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated 6 months ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 9 months ago
- Microbial agile accurate SNP Typer☆29Updated last year