Contevol 1.01 – Continuous Character Evolution Teaching Program

Contevol 1.01

:: DESCRIPTION

Contevol is a simulation program designed for my class in Evolutionary Genetics. It allows the user to simulate the evolution of a quantitative character that is controlled by 5 loci, where there is a fitness function designed by the user. The user gets to see the distribution of the values of the quantitative character in a population, generation after generation. The genotypes that make up this distribution (or at any rate a representative sample of them) are displayed in the same histogram.

::DEVELOPER

Joseph Felsenstein

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

Contevol

:: MORE INFORMATION

© Copyright 2000, 2009 by the University of Washington. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed.

Dnatree 1.3 – DNA Phylogeny Teaching Program

Dnatree 1.3

:: DESCRIPTION

DNATREE is a computer program that simulates the branching of an evolutionary tree, using a model of random branching of lineages. It then evolves a DNA sequence along this tree, and displays the resulting sequences. The user can save the tree and the sequences if they want to use them in other programs. The user can control the expected rate of evolution of the sequences per unit time, and the transition/transversion ratio.

::DEVELOPER

Joseph Felsenstein

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

Dnatree

:: MORE INFORMATION

Citation:

Kuhner, M. K. and J. Felsenstein. 1994.
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.
Molecular Biology and Evolution 11: 459-468 (Erratum 12: 525 1995).

MB 6.84 – DNA Analysis Program

MB 6.84

:: DESCRIPTION

MB ( MolecularBiological DNA Analysis) is a free Windows DNA analysis program.MB is a relative small and easy to use program. It includes the most common features for the analysis of DNA and protein sequences. These are: restriction sites search, restriction mapping, amino protein analysis, multiple sequence alignment, dot plot, molecular weight calculation and ORF search.

::DEVELOPER

MB Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

MB

:: MORE INFORMATION

MB Registration Form

DNA for Windows 2.51 – DNA Sequence Editing & Analysis Program

DNA for Windows 2.51

:: DESCRIPTION

DNA for Windows is a compact, easy to use DNA analysis program, ideal for small-scale sequencing projects.  It is particularly suited to working with chromatogram files from ABI machines, and is one of the few programs able to edit as well as view these files.  The program has powerful DNA translation and restriction enzyme analysis facilities, and works with external programs to produce multiple alignments and contigs with ease.

::DEVELOPER

David Dixon

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

DNA for Windows

:: MORE INFORMATION

If you find the program useful, don’t forget to register – you will receive the latest version which already has a number of significant improvements over the evaluation version.

AutoDock Vina 1.1.2 – Molecular Docking and Virtual Screening Program

AutoDock Vina 1.1.2

:: DESCRIPTION

AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.

::DEVELOPER

Dr. Oleg Trott , in Molecular Graphics Laboratory , The Scripps Research Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

AutoDock Vina

:: MORE INFORMATION

Citation

O. Trott, A. J. Olson,
AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading,
Journal of Computational Chemistry 31 (2010) 455-461

XPlasMap 0.99 – DNA Mapping Program

XPlasMap 0.99

:: DESCRIPTION

XPlasMap is a DNA mapping program. It draws plasmid or linear DNA maps, showing features such as genes, multiple cloning sites, and restriction sites. The maps are highly customizable: colors, styles, position, and overall appearance of features can be changed. Fragments can be copied or cut, and inserted into different maps or turned into maps on their own (virtual cloning). FastA, text, and GenBank files can be imported directly, making maps of long and complex sequences (e.g. genomic sequences) quick and easy to prepare.

::DEVELOPER

Ian York

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOS 10.4 or higher

:: DOWNLOAD

XPlasMap

:: MORE INFORMATION

XPlasMap is free (as in no cost) and can be redistributed as a complete package.

JMolDraw 0.6 Alpha – 2D Chemical Structure Drawing Program

JMolDraw 0.6 Alpha

:: DESCRIPTION

JMolDraw is a small Java-Applet for drawing organic structures on your computer. The applet also supports Im/Export of MDL-Molfiles, drawing of Query-Atoms for database search, templates and much more.

::DEVELOPER

Thomas Seidel

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

JMolDraw

:: MORE INFORMATION

License: GPL

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