santeripuranen / SpydrPickLinks
SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.
☆13Updated 3 years ago
Alternatives and similar repositories for SpydrPick
Users that are interested in SpydrPick are comparing it to the libraries listed below
Sorting:
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆24Updated 11 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated 2 years ago
- Bacterial GWAS analysis☆40Updated last month
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆22Updated 3 years ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 3 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆51Updated 2 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆28Updated 8 months ago
- Gene-flank analysis tool☆27Updated 6 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆45Updated last month
- Genomewide Epistasis Analysis on Bacteria☆14Updated last month
- IslandPath standalone software☆32Updated last year
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Detect contigs of complete circular genomes☆23Updated 6 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- ☆23Updated 4 months ago
- ☆22Updated 2 years ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated 2 years ago
- Calculate assocations between genes and traits☆23Updated 3 months ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆31Updated 4 months ago
- MAG Circularization Method☆33Updated 3 years ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆49Updated 2 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆23Updated 2 years ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆19Updated 2 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Updated 7 years ago
- Strain Resolution ON Graphs☆48Updated last year
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆36Updated 2 months ago
- Recombination-free trees☆58Updated 3 months ago
- Strain Prediction and Analysis with Representative SEquence☆19Updated 6 months ago