This package provides gzip-like compression for tskit tree sequences. Compression is lossless for supported tskit tree sequences.

SHARC is a pipeline for somatic SV calling and filtering from tumor-only Nanopore sequencing data. It performs mapping, SV calling, SV filtering, random forest classification, blacklist filtering and SV prioritization, followed by automated primer design for PCR amplicons of 80-120 bp that are useful to track cancer ctDNA molecules in liquid biopsies.

Mellon is a non-parametric cell-state density estimator based on a nearest-neighbors-distance distribution. It uses a sparse gaussian process to produce a differntiable density function that can be evaluated out of sample.

This package provides utilities for exploratory analysis of large scale genetic variation data.

This package provides a Python module to read and write the Newick format. In mathematics and phylogenetics, Newick tree format is a way of representing graph-theoretical trees with edge lengths using parentheses and commas.

sfsutils is a package for parsing SFS, with support for versatile stratification, ancestral allele and site-degeneracy annotation, and filtering. Beyond the one-dimensional spectrum it also derives the joint SFS across several populations and the two-site SFS of linked pairs of sites, and reads from VCF files, VCF-Zarr stores, and tskit tree sequences (ARGs).

This package provides a python implementation of DESeq2.

CMAPLE is a C++ reimplementation of MAPLE - a novel likelihood-based phylogenetic inference method for pandemic-scale epidemiological genomic data.

cogent3 is a Python library for the analysis of biological sequence data. We endeavour to provide a first-class experience within Jupyter notebooks, but the algorithms also support parallel execution on compute systems with 1000’s of processors.

fastdfe is a package for fast, flexible, and hierarchical inference of the DFE from SFS.

This package provides in uncompressed version of the gnomAD structural variant sites.

diemPy is a computational tool designed to polarize genomic data for hybrid zone analysis. The package implements an expectation-maximization (EM) algorithm to determine the optimal polarization of genetic markers, enabling researchers to identify and analyze patterns of introgression and hybridization in genomic datasets.

This package provides a phylogeny dating method using least-squares algorithms and criteria.

The Spliced Transcripts Alignment to a Reference (STAR) software is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.

SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.

This module provides code coverage metrics for Perl. Code coverage metrics describe how thoroughly tests exercise code. By using Devel::Cover you can discover areas of code not exercised by your tests and determine which tests to create to increase coverage.

This package provides tools for rapid prokaryotic genome annotation.

SeqAn is a C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It contains algorithms and data structures for string representation and their manipulation, online and indexed string search, efficient I/O of bioinformatics file formats, sequence alignment, and more.

This package is designed to help the scientist, engineer, statistician, etc., to construct appropriate experimental designs.

The carputils framework will be the optimal way to access openCARP for most users. This Python framework was developed to provide the means to easily encode in silico experiments including pre- and postprocessing. carputils will call the openCARP simulator.

This package is designed to help the scientist, engineer, statistician, etc., to construct appropriate experimental designs.

Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

Atomes is a toolbox developed to analyze, to visualize and to create/edit three-dimensional atomistic models. It offers a workspace that allows users to have many projects opened simultaneously.