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Top : Software : Scientific : Biology : Miscelleanous

Chess in a Few Bytes
Linux has a good range of extremely strong chess engines such as Stockfish, Critter, Togo II, Crafty, GNU Chess, and Komodo. The chess engines featured in this article offer no match to a good chess engine, but they show how much can be achieved with a minuscule codebase.

(Read more)
Penguin Command
Penguin Command is a clone of the classic Missile Command game, but it has more advanced graphics and sound. The gameplay has also been slightly modified. Read more


  • Adun
    Adun is an extensible biomolecular simulation program that includes data management and analysis capabilities.
  • Clarrhmos
    Clarrhmos is a cell automata description language and simulation program for models of myocardial electrophysiology.
  • Clustal X
    This package offers a GUI interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence- and profile-alignments to analyse the results. The sequence alignment is displayed in a window on the screen.
  • Consed
    Consed is a graphical Tool for Editing Phrap Assemblies.
  • ConSole
    Constance System for Online EEG (ConSole) is a free and open-source application to build and run realtime EEG experiments.
  • CTSim
    CTSim simulates the process of transmitting X-rays through phantom objects. These X-ray data are called projections. CTSim reconstructs the original phantom image from the projections using a variety of algorithms. Additionally, CTSim has a wide array of image analysis and image processing functions.
    DIALIGN is a software program for multiple alignment developed by Burkhard Morgenstern et al. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing whole segments of the sequences. No gap penalty is used.
  • Finomaton
    Finomaton lets you comfortably draw and typeset finite state machines (automata). It outputs plain MetaPost-code which can be transformed to PostScript and subsequently included in your TeX and LaTeX documents for excellent typesetting quality.
  • FIRM
    FIRM is an interactive program (fortran) for calculating NOEs of a structural model using the relaxation matrix approach.
  • FreeDiams
    FreeDiams is a program for making prescriptions of pharmaceutical drugs and testing their interactions. It is the result of building the FreeMedForms prescriber plugins into a standalone application.
  • GTdb
    GTdb is a modular genotype database for all markers and organisms. The database has core which captures information common to different variation measurements and extensions to method and instrument specific data.
  • gtkdive
    gtkdive was written to learn about the Buehlmann ZH-L16 model that deals with accumulation of inert gas in body tissues.
  • MetaPath
    MetaPath is a tool for the analysis of metabolic pathway and associated visualisation of experimental data. Built on the MetaCyc database it provides an interactive map in which multiple pathways can be simultaneously visualised.
  • Micro-Manager
    Micro-Manager is a software package for microscope image acquisition. It controls a number of scientific grade cameras, shutters, filter wheels, stages, and other devices. It enables the acquisition of time-lapses, z-stacks, and multi-channel images.
  • mkESA
    mkESA is a program for constructing enhanced suffix arrays (ESAs) from biological sequence data. The program is based on an implementation of Manzini's lightweight Deep-Shallow algorithm, which can also utilize multiple CPUs/cores for extra performance.
    MUSCLE stands for MUltiple Sequence Comparison by Log- Expectation. MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. Read more
  • NDEE
    NDEE is for the evaluation of n-dimensional NMR-data. The ability to combine structural and dynamic information is one of the most important attributes of NMR in structural molecular biologic context.
  • OpenVista
    OpenVista is the open-source version of VistA, which is a healthcare information system developed by the U.S. Department of Veterans Affairs (the "VA") to drive all their hospitals and clinics.
  • Paup
    (commercial) Paup is for the inference of evolutionary trees.
  • Pyvox
    Pyvox (formerly known as BBLimage) is a set of software tools for medical image processing, particularly skull stripping and segmentation of MR brain images; tools to support other applications may be added later. These tools are intended to support researchers who need to prototype new image analysis algorithms or to develop automated image analysis tools for specific image analysis applications.
  • QDist
    QDist implements a sub-cubic algorithm for computing the quartet distance between between general trees (i.e. the trees are not required to be binary).
  • ScalaBLAST
    ScalaBLAST is a high-performance multiprocessor implementation of the NCBI BLAST library. It supports all 5 primary program types (blastn, blastp, tblastn, tblastx, and blastx) and several output formats (pairwise, tabular, and XML).
  • SIBsim4
    SIBsim4 is an extensive rewrite of the sim4 program to improve execution speed and provide more informative output. Written in C, mainly targeted at Linux and Unix.
  • SimThyr
    SimThyr is a continuous simulation program for pituitary-thyroid feedback control.
  • simuPOP
    simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. Read more
    SPINA is software for determining constant structure-parameters of endocrine feedback control systems from hormone levels obtained in vivo.
  • SwissParser
    SwissParser allows you to build parsers for typical bioinformatics flat-file "database"
  • ThermonucleotideBLAST
    ThermonucleotideBLAST is a software program for searching a target database of nucleic acid sequences using an assay specific query that is based on biochemical assays (i.e. a pair of oligonucleotide sequences representing PCR primers or Padlock probes, a triplet of oligos representing PCR primers and a TaqMan probe, or a single oligo representing a hybridization probe). Unlike existing programs (i.e. BLAST) which use heuristic measures of sequence similarity for identifying matches between a query and target sequence, ThermonucleotideBLAST uses free energy and melting temperature.
    TREE-PUZZLE (previously known as PUZZLE) is an interactive console program that implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Read more
  • TreeView X
    TreeView X is an open source and multi-platform program to display phylogenetic trees. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). Read more
  • Trio
    Trio is a conversion program that provides the ability to read and write molecular dynamics trajectory files in several common formats. It is a small standalone program, and should be easy to compile and run on almost any system.

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