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ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.

HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing data. It is the core library used by samtools and bcftools.

Jalview is a multiple alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) and is also available as a general purpose alignment editor. o Reads and writes alignments in a variety of formats o Gaps can be inserted/deleted using the mouse. o Group editing (insertion deletion of gaps in groups of sequences). o Removal of gapped columns. o Align sequences using Web Services (Clustal, Muscle...) o Amino acid conservation analysis similar to that of AMAS. o Alignment sorting options (by name, tree order, percent identity, group). o UPGMA and NJ trees calculated and drawn based on percent identity distances. o Sequence clustering using principal component analysis. o Removal of redundant sequences. o Smith Waterman pairwise alignment of selected sequences. o Web based secondary structure prediction programs (JNet). o User predefined or custom colour schemes to colour alignments or groups. o Sequence feature retrieval and display on the alignment. o Print your alignment with colours and annotations. o Output alignments as HTML pages, images (PNG) or postscript (EPS). If you use Jalview in your work, please quote this publication. Clamp, M., et al. (2004), The Jalview Java Alignment Editor. Bioinformatics, 12, 426-7

LibSBML is an open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It is not an application itself (though it does come with example programs), but rather a library you can embed in your own applications. LibSBML understands all Levels and Versions of SBML, as well as the SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in ISO C and C++ but can be used from all the languages listed in the right-hand box.

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. The library is licensed under the 3-clause BSD license except the applications which are GPL. This port now only contains the header library and API documentation. The apps are separate.

Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer.

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. This port contains applications built on SeqAn and developed within the SeqAn project. Among them are famous read mappers like RazerS and Yara, as well as many other tools. Some applications are packaged separately and the library can be found at biology/seqan.

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. This port includes only the library, the apps have been moved to biology/seqan-apps. This is the last release of the version 1 API, it is highly recommended to upgrade to biology/seqan (version 2).

From the website: T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Related publications: - 3DCoffee: Combining Protein Sequences and Structures within Multiple Sequence Alignments. O. O'Sullivan, K Suhre, C. Abergel, D.G. Higgins, C. Notredame. Journal of Molecular Biology, Vol 340, pp385-395, 2004 - T-Coffee: A novel method for multiple sequence alignments. C.Notredame, D. Higgins, J. Heringa, Journal of Molecular Biology,Vol 302, pp205-217,2000 - COFFEE: A New Objective Function For Multiple Sequence Alignmnent. C. Notredame, L. Holme and D.G. Higgins,Bioinformatics,Vol 14 (5) 407-422,1998

BRL-CAD is a powerful Combinatorial/Constructive Solid Geometry (CSG) solid modeling system that includes an interactive geometry editor, ray-tracing support for rendering and geometric analysis, network-distributed framebuffer support, image and signal-processing tools, and an embedded scripting language. The package is a collection of over 400 tools and utilities across over 750,000 lines of source code. Included is support for various geometric data format conversions, image and signal processing capabilities, sophisticated ray-tracing based lighting models, network distributed ray-tracing, massively parallel ray-tracing, animation capabilities, data compression, image handling, and interactive 3-D geometric editing. Included is an implementation of Weiler's n-Manifold Geometry (NMG) data structures for surface-based solid models and photon mapping.