santeripuranen / SpydrPickView external linksLinks
SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.
☆15Apr 29, 2022Updated 3 years ago
Alternatives and similar repositories for SpydrPick
Users that are interested in SpydrPick are comparing it to the libraries listed below
Sorting:
- Genomewide Epistasis Analysis on Bacteria☆15May 13, 2025Updated 9 months ago
- A tool for the identification of coincident (associating and dissociating) genes in pangenomes.☆110Oct 20, 2023Updated 2 years ago
- Plasmid analysis using rearrangement distances☆50Jan 23, 2026Updated 3 weeks ago
- Locus and lineage tests for bacterial GWAS☆28Oct 5, 2017Updated 8 years ago
- ☆18Jun 11, 2024Updated last year
- Quantifying the significance of genetic variation using probabilistic profile-based methods.☆19Apr 21, 2021Updated 4 years ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆94Dec 9, 2025Updated 2 months ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆68Sep 19, 2022Updated 3 years ago
- Recombination-free trees☆63Sep 1, 2025Updated 5 months ago
- R integration for edlib, a C/C++ library for pairwise sequence alignment using edit distance (Levenshtein distance).☆11Jul 20, 2025Updated 6 months ago
- A Simulator for Bacterial Machine learning and Genome-Wide Association Studies☆22Jul 21, 2021Updated 4 years ago
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago
- For bluntifying overlapped GFAs☆13Jul 26, 2024Updated last year
- mGEMS Genomic epidemiology with mixed samples☆15Sep 4, 2024Updated last year
- Assort phage protein sequences into phamilies using MMseqs2☆11Dec 16, 2024Updated last year
- Factorize metagenotypes to infer strains and their abundances☆12Sep 29, 2024Updated last year
- Uses cDBG to count unitigs in bacterial populations☆16Feb 15, 2023Updated 3 years ago
- Building the compacted de Bruijn graph efficiently from references or reads.☆92Jan 29, 2026Updated 2 weeks ago
- ☆13Sep 4, 2017Updated 8 years ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids using protein structural information☆35Updated this week
- FFPopSim is a collection of C++ classes and a Python interface for efficient simulation of large populations, in particular when the prod…☆14Oct 14, 2025Updated 4 months ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆103Feb 9, 2026Updated last week
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆41Apr 17, 2024Updated last year
- strain-level analysis tools☆39Oct 21, 2024Updated last year
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆166Apr 16, 2025Updated 10 months ago
- A pipeline for construction and graphical visualization of annotated pangenome networks.☆16Oct 24, 2018Updated 7 years ago
- Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop☆72Jul 31, 2025Updated 6 months ago
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆46Jan 27, 2026Updated 3 weeks ago
- MetaSNV, a metagenomic SNV calling pipeline.☆20Mar 25, 2022Updated 3 years ago
- Follow up to Grace Blackwell's 661k dataset, for 2023☆130Updated this week
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆186Feb 6, 2026Updated last week
- A tool for removing redundant genomes from a set of assemblies☆78Sep 10, 2025Updated 5 months ago
- Code for the paper "Learning the fitness dynamics of pathogens from phylogenies"☆23Nov 24, 2025Updated 2 months ago
- Color DNA/RNA bases in terminal output☆21Aug 29, 2017Updated 8 years ago
- Pipeline for analysing intergenic regions in bacteria☆39Oct 25, 2019Updated 6 years ago
- Efficient phylogenetic tree inference for massive taxonomic datasets☆141Apr 6, 2025Updated 10 months ago
- Bacterial phylogenetics in BEAST 2.☆18Mar 30, 2023Updated 2 years ago
- Evaluating Nanopore-based bacterial variant calling☆21Jul 23, 2025Updated 6 months ago
- A library and tool for accessing remote BLOW5 files.☆24Feb 5, 2026Updated last week