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 new way of computing bootstrap supports in large phylogenies.

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.

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

IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data such as:

• Recombination model probability distribution

• Hypermutation model

• Best candidates recombination scenarios

• Generation probabilities of sequences (even hypermutated)

Its heavily object oriented and modular style was designed to ensure long term support and evolvability for new tasks in assessing TCR and BCR receptors features using modern parallel architectures.

This package provides a python implementation of DESeq2.

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.

Biosoup is a C++ collection of header-only data structures used for storage and logging in bioinformatics tools.

Easel is an ANSI C code library developed by the Eddy/Rivas laboratory at Harvard. Easel supports our work on computational analysis of biological sequences using probabilistic models. Easel is used by HMMER, the profile hidden Markov model software that underlies several protein and DNA sequence family databases such as Pfam, and by Infernal, the profile stochastic context-free grammar software that underlies the Rfam RNA family database. Easel aims to make similar applications more robust and easier to develop, by providing a set of reusable, documented, and well-tested functions.

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

A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes. It includes ten models added to the metagenome mode:

• Acanthamoeba polyphaga mimivirus

• Paramecium bursaria Chlorella virus

• Acanthocystis turfacea Chlorella virus

• VirSorter2's NCLDV gene model

• Topaz (genetic code 15)

• Agate (genetic code 15)

• Gut phages (genetic code 15)

• Gut phages (genetic code 11) x 5

MCView creates a Shiny app facilitating interactive exploration and annotation of Metacell models.

Control-FREEC automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. The control (matched normal) sample is optional for whole genome sequencing data but mandatory for whole exome or targeted sequencing data. For whole genome sequencing data analysis, the program can also use mappability data (files created by GEM).

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.

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

Scriabin aims to provide a comprehensive view of cell-cell communication (CCC). It achieves this without requiring subsampling or aggregation.

This package contains a set of common Perl utilities for generating consistent Vcf headers. It primarily exists to prevent code duplication between some other projects.

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.

This packages provides a collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.

Anvi’o is a comprehensive platform that brings together many aspects of today’s computational strategies of data-enabled microbiology, including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-use fashion through extensive interactive visualization capabilities.