lczech / genesis
A library for working with phylogenetic and population genetic data.
☆57Updated last week
Related projects ⓘ
Alternatives and complementary repositories for genesis
- A toolkit for analyzing and visualizing phylogenetic (placement) data☆57Updated 4 months ago
- Massively parallel phylogenetic placement of genetic sequences☆78Updated 2 years ago
- A fast tool for hybrid genome assembly of long and short reads☆76Updated 4 years ago
- A bioinformatic toolkit to align genome assemblies into pangenome graphs☆90Updated 2 weeks ago
- mapDamage: tracking and quantifying damage patterns in ancient DNA sequences☆43Updated 2 months ago
- phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.☆77Updated last year
- Collection of scripts for bacterial genomics☆44Updated 4 years ago
- Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.☆46Updated 2 years ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆108Updated 6 months ago
- Ancestral character reconstruction and visualisation for rooted phylogenetic trees☆32Updated 2 months ago
- r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)☆63Updated 11 months ago
- 🔗Genome assembly scaffolder using minimizer graphs☆83Updated last month
- Hybrid error correction of long reads using colored de Bruijn graphs☆96Updated last month
- Chromosome-level scaffolding using multiple references☆157Updated 2 months ago
- Inference of microbial interaction networks from large-scale heterogeneous abundance data☆74Updated 5 months ago
- A toolbox for pangenome analysis and threshold evaluation.☆91Updated 2 years ago
- A toolkit for annotation of transposable element families from unassembled sequence reads☆31Updated last year
- ✏️ Genome assembly polishing & SNV detection☆64Updated this week
- A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.☆27Updated last month
- A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads☆69Updated 3 years ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆83Updated last month
- Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)☆48Updated 9 years ago
- Best-fit model selection☆77Updated 8 months ago
- SEER, reimplemented in python 🐍🔮☆111Updated last month
- A genomic k-mer counter (and sequence utility) with nice features.☆117Updated 2 weeks ago
- Posterior summarisation in Bayesian phylogenetics☆55Updated 2 months ago
- Evaluate variant calls and its combination with k-mer multiplicity☆64Updated last year
- A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concat…☆53Updated 3 months ago
- GenMap - Fast and Exact Computation of Genome Mappability☆100Updated 5 months ago
- software for UCE (and general) phylogenomics☆80Updated 2 weeks ago