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.

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.

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.

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 Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

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.

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

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.

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).

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

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.

SPAdes is an assembly toolkit containing various assembly pipelines.

Bioparser is a C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.

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

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

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

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