ACFTools is a utility for manipulating X-Plane flight simulator aircraft and weapon models without using its Plane Maker. It can decode both Apple and Intel ACF/WPN formats into plain text files with a syntax similar to C, which can be edited and then re-converted into binary data. It is able to extract almost complete 3D models of aircraft (fuselage, floats, tanks, wings, stabs, propellers, engines) and write it in AC3D modeler format. Edited 3D parts can then be merged into plain text and consequently converted into binary ACF files.

AGM Build is a molecular builder and conformational editor. It can be used for interactive model preparation for molecular dynamics simulations, including association of atom types and partial charges. It features geometry editing, lattice building, building of chain molecules (e.g. proteins), chains with predetermined conformations, and charges and atom types according to selected Force Field.

ASCIIMathML is a script that converts calculator-style ASCII math notation (and many LaTeX formulas) to Presentation MathML while your Web page loads. It works with HTML and XHTML files in Mozilla/Firefox/Netscape 7+ browsers, as well as in Internet Explorer 6 with MathPlayer. For example, the solutions for the equation 'ax^2+bx+c=0' are expressed in the HTML file as '(-b +- sqrt(b^2 - 4ac))/(2a)', and display as nicely formatted MathML. The script can be easily used in wikiservers and blogs, as a rudimentary MathML editor (with instant preview), and to preview math formulas as they are typed into a Web page input area.

Algraeph is a tool for manual alignment of linguistic graphs, such as phrase structure trees or dependency structures, where each node corresponds to a subsequence of the analyzed input sentence. It allows you to express the similarity between two graphs by aligning their nodes and attaching relation labels to these alignments. Graphs are read from one or more graphbanks (or treebanks) in the GraphML or Alpino formats. Alignment relations are user-defined and are stored in a simple XML format, which can be used for further processing. The resulting parallel graph corpus is a useful data set for many tasks in computational linguistics and natural language processing.

AnimalTracker can be used to track the position of animals and their behavior in the context of an observation. Users can draw a map of the area and position the animals on it. The application can then calculate the distance between the animals and the distribution of them on the map across a specified time period. All data can be exported as tables to be used in spreadsheet applications or statistics programs.

Animath is a 2D/3D Finite Element Method library entirely implemented in C++. It is suited for fluid-structure interaction simulation, and it is mathematically based on higher-order tetrahedral/triangular elements. It provides front-ends to matrix solvers and mesh generators.

Asymptote is a powerful descriptive 2D and 3D vector graphics language for technical drawing, inspired by MetaPost but with an improved C++-like syntax. It provides for figures the same high-quality level of typesetting that LaTeX does for scientific text. Asymptote is a programming language as opposed to just a graphics program. It can exploit the best features of script (command-driven) and graphical user interface (GUI) methods. High-level graphics commands are implemented in the language itself, allowing them to be easily tailored to specific applications.