Purdue University

Basenji is a tool for sequential regulatory activity predictions with deep convolutional neural networks.

BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.

Bazam is a tool to extract paired reads in FASTQ format from coordinate sorted BAM files.

bbFTP is a file transfer software. It implements its own transfer protocol, which is optimized for large files (larger than 2GB) and secure as it does not read the password in a file and encrypts the connection information.

Bbmap is a short read aligner, as well as various other bioinformatic tools.

BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.

Bcftools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF.

bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.

Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.

BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.

Bedops is a software package for manipulating and analyzing genomic interval data.

Bedtools is an extensive suite of utilities for genome arithmetic and comparing genomic features in BED format.

Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzipped BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.

Biobambam is a collection of tools for early stage alignment file processing.

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming.

Biopython is a set of freely available tools for biological computation written in Python.

Bismark is a tool to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.

Blasr is a read mapping program that maps reads to positions in a genome by clustering short exact matches between the read and the genome, and scoring clusters using alignment.

BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.