neherlab / ffpopsim
FFPopSim is a collection of C++ classes and a Python interface for efficient simulation of large populations, in particular when the product of mutation rate and population size is larger than one. It consists of one library for individual-based simulations, and a complementary one for simulation of the entire genotype distribution. The latter i…
☆14Updated last year
Alternatives and similar repositories for ffpopsim:
Users that are interested in ffpopsim are comparing it to the libraries listed below
- Work for the tree sequence inference paper.☆23Updated 4 years ago
- pathoscore evaluates variant pathogenicity tools and scores.☆21Updated 2 years ago
- Metalign: efficient alignment-based metagenomic profiling via containment min hash☆33Updated last year
- Prediction fitness of leaves on a genealogical tree☆11Updated 9 years ago
- Classify sequencing reads using MinHash.☆48Updated 4 years ago
- Bioinformatics Open Source Sequence machine☆33Updated last year
- A collection of documented examples using TreeTime☆20Updated 5 years ago
- Build an index for your BAM Index (BAI)☆17Updated 9 years ago
- Homebrew formulae for bioinformatics software only available for Linux☆27Updated 5 years ago
- Samwell: a python package for using genomic files... well☆20Updated 2 years ago
- drunk on perbase pileups and lua expressions☆17Updated last year
- Annotating principal splice isoforms☆14Updated 5 months ago
- ☆14Updated 2 years ago
- MAVE-NN: genotype-phenotype maps from multiplex assays of variant effect☆25Updated last month
- Hitting associations with k-mers☆45Updated 2 years ago
- A collection of publications on comparison of high-throughput sequencing technologies.☆26Updated 2 months ago
- k-mer similarity analysis pipeline☆20Updated last month
- A toolkit for annotation of transposable element families from unassembled sequence reads☆30Updated last year
- dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organ…☆20Updated last month
- MAPLE - a new approximate approach for maximum likelihood phylogenetics at short divergence.☆48Updated this week
- IMSEQ - IMmunogenetic SEQuence Analysis☆15Updated 6 years ago
- Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3☆38Updated 2 years ago
- Interactive demonstration of how to use PCA, t-SNE, and UMAP on genotype data from the Thousand Genome Project.☆20Updated 4 years ago
- Library for indexing VCF files for random access searches by rsID☆17Updated last year
- PiGx SARS-CoV-2 wastewater sequencing pipeline☆18Updated last year
- The software involved in the MetaPhase project, as described in G3 (http://dx.doi.org/10.1534/g3.114.011825)☆16Updated 6 years ago
- Fast calculations of linkage-disequilibrium in large-scale human cohorts☆43Updated 5 years ago
- genotype dimensionality reduction with a VAE☆43Updated 10 months ago
- http://www.combio.pl/alfree☆23Updated 2 years ago
- reference free variant assembly☆33Updated last year