MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets.

CAT and BAT are pipelines for the taxonomic classification of long DNA sequences and MAGs of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files are formated appropriately.

This package provides a tool to extract assembly statistics from FASTA and FASTQ files.

This package provides a subset of the Regulatory Sequence Analysis Tools (RSAT).

This package provides a fast interval tree-like implementation in C, wrapped for the Python ecosystem.

Kastore is a simple storage format mapping keys to numerical arrays in a write-once-read-many file store.

The CodeMin minimization library provides a set of lightweight minimization functions originally developed for the CodeAxe phylogenetic analysis package.

This package provides an interface for the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. This includes interfaces to blastn, blastp, blastx, and makeblastdb.

This package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenburg.

The goal of NicheNet is to study intercellular communication from a computational perspective. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with a prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest.

SPAdes is an assembly toolkit containing various assembly pipelines.

pyslim is a small python package to help analyse and manipulate tree sequences produced by SLiM, e.g., to identify individuals alive at a particular time, or to recapitate the results of a SLiM simulation.

The IQ-TREE software was created as the successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the rapid accumulation of phylogenomic data, leading to a need for efficient phylogenomic software that can handle a large amount of data and provide more complex models of sequence evolution. To this end, IQ-TREE can utilize multicore computers and distributed parallel computing to speed up the analysis. IQ-TREE automatically performs checkpointing to resume an interrupted analysis.

As input IQ-TREE accepts all common sequence alignment formats including PHYLIP, FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a self-readable report file (name suffix .iqtree), a NEWICK tree file (.treefile) which can be visualized by tree viewer programs such as FigTree, Dendroscope or iTOL.

Key features of IQ-TREE:

• Fast and effective stochastic algorithm to reconstruct phylogenetic trees by maximum likelihood;

• An ultrafast bootstrap approximation (UFBoot) to assess branch supports;

• An ultrafast and automatic model selection (ModelFinder);

• A flexible simulator (AliSim) which can simulate sequence alignments under more realistic models than Seq-Gen and INDELible;

• Several fast branch tests like SH-aLRT and aBayes test and tree topology tests like the approximately unbiased (AU) test.

This package provides IQ-TREE version 3.

Vcztools provides a Python API to efficiently read VCZ data from local files and remote object stores using bcftools-compatible region and variant filtering syntax. It aims to provide a drop-in replacement for a subset of bcftools functionality.

This package provides a library for reading BAM files quickly into dataframes in Python.

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.

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

FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.

Succinct tree sequences are an efficient way of representing the genetic history - often technically referred to as an Ancestral Recombination Graph or ARG - of a set of DNA sequences.

The tree sequence format is output by a number of external software libraries and programs (such as msprime, SLiM, fwdpp, and tsinfer) that either simulate or infer the evolutionary ancestry of genetic sequences. This library provides the underlying functionality that such software uses to load, examine, and manipulate ARGs in tree sequence format, including efficientaccess to the correlated sequence of trees along a genome and general methods to calculate genetic statistics.

This package provides utilities for comparing ARGs represented as tree sequences. It includes tooling to quantify similarities and differences between ARG topologies, haplotype paths, and related structures.

ancestree is a package for likelihood-based, per-site ancestral-allele annotation, unifying outgroup-based (EST-SFS-style) and ARG-based (PolarBEAR-style) inference behind a single likelihood kernel. It runs in three modes: fixed-tree, ARG, and local-tree, the last inferring its own local genealogies from the variant data rather than taking a supplied ARG. Every site receives a full posterior over the four nucleotide states, with multi-allelic sites, missing data and recurrent mutation handled natively.