This package contains a collection of bioinformatics data structures and algorithms. It provides I/O classes, bitio classes, text indexing classes and BAM sequence alignment functionality.

The demes Python package provides an API for defining, parsing, and sharing Demes demographic models. Applications can use demes to parse human-readable Demes YAML files into fully-resolved demographic models. In addition, demes provides convenient data structures to simplify manipulation of demographic models.

Primer3-py is a Python-abstracted API for the popular Primer3 library. The intention is to provide a simple and reliable interface for automated oligo analysis and design.

Primer3-py also includes bindings for the Primer3 primer design engine if you’d prefer to use an established pipeline. The IO parameters mirror those of the original Primer3, but you don’t have to deal with messy and slow file IO for your automated workflows.

bio2zarr efficiently converts common bioinformatics formats to Zarr format.

Tools:

• vcf2zarr converts VCF data to VCF Zarr format;

• plink2zarr converts PLINK 1.0 data to VCF Zarr format;

• tskit2zarr converts tskit data into VCF Zarr format;

• vcfpartition is a utility to split an input VCF into a given number of partitions;

• zipzarr is a utility for zipping/unzipping Zarr directory stores.

tstrait is a Python package to simulate quantitative traits from a given tree sequence.

This package computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller.

Build contrasts for models defined with formulaic.

Framework for analyzing low-depth NGS data in heterogeneous/structured populations using PCA. Population structure is inferred by estimating individual allele frequencies in an iterative approach using a truncated SVD model. The covariance matrix is estimated using the estimated individual allele frequencies as prior information for the unobserved genotypes in low-depth NGS data.

The estimated individual allele frequencies can further be used to account for population structure in other probabilistic methods. pcangsd can be used for the following analyses:

• Covariance matrix

• Admixture estimation

• Inbreeding coefficients (both per-sample and per-site)

• HWE test

• Genome-wide selection scans

• Genotype calling

• Estimate NJ tree of samples

phasegen is a package for computation and inference on exact solutions of coalescent distributions under diverse demographic scenarios. phasegen leverages phase-type theory and supports a wide range of demographic models and coalescent tree statistics.

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

SINGER is a Bayesian method to do posterior sampling of ARG under Sequentially Markovian Coalescent. SINGER works by iterative threading one haplotype to the partially-built ARG, until the ARG for all haplotypes have been built. After initialization, MCMC will be performed to update the ARG to explore the posterior distribution.

This package provides tools for filtering on quality and/or read length, and optional trimming after passing filters. Reads from stdin, writes to stdout. Optionally reads directly from an uncompressed file specified on the command line. It is intended to be used directly after fastq extraction, prior to mapping, or in a stream between extraction and mapping.

Primer3 is a widely used program for designing PCR primers. PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.

sgkit is a Python package that provides a variety of analytical genetics methods through the use of general-purpose frameworks such as Xarray, Pandas, Dask and Zarr. The sgkit API makes as few assumptions as possible about the origin, structure, and intended use of genetic data by adopting a set of domain-specific conventions that allow such data to be used within this broader ecosystem of tools. The package is designed for complex workflows over large distributed datasets but attempts to make it as easy as possible to scale down to smaller datasets and access simpler functionality for those that may be new to Python (though there is still a good bit of work to done on this front).

This package provides procedures to calculate statistics for Oxford Nanopore sequencing data and alignments.

This package provides an implementation of the CaVEMan program. It uses an expectation maximisation approach to calling single base substitutions in paired data. It is designed for use with a compute cluster. Most steps in the program make use of an index parameter. The split step is designed to divide the genome into chunks of adjustable size to optimise for runtime/memory usage requirements.

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 2.