is a command-line genome browser running from terminal window and solely based on ASCII characters.

(Open Java Development Kit) is a free and open source implementation of the Java Platform, Standard Edition (Java SE).

a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture.

an extension to Brian Kernighan's awk, with added support for several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q, and TAB-delimited formats with column names along with new built-in functions and a command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk should behave exactly like the original BWK awk.

is a set of fast and accurate sequence read classification tools designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. This is done by using a reference set of full-length ribosomal RNA sequences for which known taxonomies are known, and for which a set of high quality OTU clusters has been previously generated. For each read, the best guess and correspoding confidence in the assignment is shown at each taxonomic and OTU level.

a set of tools for biological computation written in Python by an international team of developers.

an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.