Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This library provides phylogenetics-related modules.

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

BioRuby comes with a comprehensive set of Ruby development tools and libraries for bioinformatics and molecular biology. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.

Segemehl is software to map short sequencer reads to reference genomes. Segemehl implements a matching strategy based on enhanced suffix arrays (ESA). It accepts fasta and fastq queries (gzip'ed and bgzip'ed). In addition to the alignment of reads from standard DNA- and RNA-seq protocols, it also allows the mapping of bisulfite converted reads (Lister and Cokus) and implements a split read mapping strategy. The output of segemehl is a SAM or BAM formatted alignment file.

Proteinortho is a tool to detect orthologous genes across different species. For doing so, it compares similarities of given gene sequences and clusters them to find significant groups. The algorithm was designed to handle large-scale data and can be applied to hundreds of species at once.

BWA-PSSM is a probabilistic short genomic sequence read aligner based on the use of position specific scoring matrices (PSSM). Like many of the existing aligners it is fast and sensitive. Unlike most other aligners, however, it is also adaptible in the sense that one can direct the alignment based on known biases within the data set. It is coded as a modification of the original BWA alignment program and shares the genome index structure as well as many of the command line options.

PiGX ChIPseq is an analysis pipeline for preprocessing, peak calling and reporting for ChIP sequencing experiments. It is easy to use and produces high quality reports. The inputs are reads files from the sequencing experiment, and a configuration file which describes the experiment. In addition to quality control of the experiment, the pipeline enables to set up multiple peak calling analysis and allows the generation of a UCSC track hub in an easily configurable manner.

PiGx is a collection of genomics pipelines. It includes the following pipelines:

• PiGx BSseq for raw fastq read data of bisulfite experiments

• PiGx RNAseq for RNAseq samples

• PiGx scRNAseq for single cell dropseq analysis

• PiGx ChIPseq for reads from ChIPseq experiments

All pipelines are easily configured with a simple sample sheet and a descriptive settings file. The result is a set of comprehensive, interactive HTML reports with interesting findings about your samples.

MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It contains modules for a large number of common bioinformatics tools.

This package provides several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable called bam.

This package is a Python wrapper for Aaron Quinlan's BEDtools programs, which are widely used for genomic interval manipulation or "genome algebra". pybedtools extends BEDTools by offering feature-level manipulations from with Python.

Bloom-filter-based error correction solution for high-throughput sequencing reads (BLESS) uses a single minimum-sized bloom filter is a correction tool for genomic reads produced by Next-generation sequencing (NGS). BLESS produces accurate correction results with much less memory compared with previous solutions and is also able to tolerate a higher false-positive rate. BLESS can extend reads like DNA assemblers to correct errors at the end of reads.

This package allows building the hierarchy of domains starting from Hi-C data. Each hierarchical level is identified by a minimum value of physical insulation between neighboring domains.

The SRA Toolkit from NCBI is a collection of tools and libraries for reading of sequencing files from the Sequence Read Archive (SRA) database and writing files into the .sra format.

CIRI-long is a package for circular RNA identification using long-read sequencing data.

GEMMA provides a standard linear mixed model resolver with application in GWAS.

METAL is a tool for meta-analysis genomewide association scans. METAL can combine either test statistics and standard errors or p-values across studies (taking sample size and direction of effect into account). METAL analysis is a convenient alternative to a direct analysis of merged data from multiple studies. It is especially appropriate when data from the individual studies cannot be analyzed together because of differences in ethnicity, phenotype distribution, gender or constraints in sharing of individual level data imposed. Meta-analysis results in little or no loss of efficiency compared to analysis of a combined dataset including data from all individual studies.

StringTie is a fast and efficient assembler of RNA-Seq sequence alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments of longer sequences that have been assembled from those reads. To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs.

This package implements a bioinformatics algorithm for demultiplexing multiplexed single cell datasets. It is built on a statistical model of tag read counts derived from the physical mechanism of tag cross-contamination.

LibSBML is a library to help you read, write, manipulate, translate, and validate SBML files and data streams. The Systems Biology Markup Language (SBML) is an interchange format for computer models of biological processes. SBML is useful for models of metabolism, cell signaling, and more. It continues to be evolved and expanded by an international community.

This package performs a fast Wilcoxon rank sum test and auROC analysis.

This package provides a Variant Effect Predictor, which predicts the functional effects of genomic variants. It also provides Haplosaurus, which uses phased genotype data to predict whole-transcript haplotype sequences, and Variant Recoder, which translates between different variant encodings.

DNA Features Viewer is a Python library to visualize DNA features, e.g. from GenBank or Gff files, or Biopython SeqRecords.