POPGENE 1.32 – Population Genetic Analysis

POPGENE 1.32

:: DESCRIPTION

POPGENE is a user-friendly computer freeware for the analysis of genetic variation among and within populations using co-dominant and dominant markers. This package provides the Windows graphical user interface that makes population genetics analysis more accessible for the casual computer user and more convenient for the experienced computer user. Simple menus and dialog box selections enable you to perform complex analyses and produce scientifically sound statistics, thereby assisting you to adequately analyze population genetic structure using the target markers.

::DEVELOPER

POPGENE Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 POPGENE

:: MORE INFORMATION

ProtEvol 1.0 – Maximum Likelihood Phylogenetic Inference with Selection on Protein Folding Stability

ProtEvol 1.0

:: DESCRIPTION

The program ProtEvol performs two kinds of computation.

  1. It computes the mean-field site-specific amino acid distributions that have minimal differences with respect to the background distribution and that constraint the average stability of the native state of the protein against both unfolding and misfolding. The program also computes an exchangeability matrix derived from an empirical substitution model or from a mutation model that can be used together with the site-specific distributions for applications in phylogenetic inference.
  2. It simulates protein evolution subject to the constraint of selection on the folding stability of the native state of the protein against both unfolding and misfolding.

::DEVELOPER

Unidad de Bioinformatica CBMSO

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  ProtEvol

:: MORE INFORMATION

Citation

Maximum likelihood phylogenetic inference with selection on protein folding stability.
Arenas M, Sánchez-Cobos A, Bastolla U.
Mol Biol Evol. 2015 Apr 2. pii: msv085.

SimPlot 3.5.1 – Sequence Similarity Plotting

SimPlot 3.5.1

:: DESCRIPTION

SimPlot (Similarity Plotting) (as well as bootscanning, quick tree generation, and informative-sites analysis) is a popular tool for recombination analysis.

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SimPlot if you cannot make that work, please email me for a download link

:: MORE INFORMATION

Reference to the paper in which author first described SimPlot

Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC.
Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.
J Virol. 1999 Jan;73(1):152-60.

SecretomeP 2.0 – Prediction of Non-classical Protein Secretion

SecretomeP 2.0

:: DESCRIPTION

SecretomeP server produces ab initio predictions of non-classical i.e. not signal peptide triggered protein secretion. The method queries a large number of other feature prediction servers to obtain information on various post-translational and localizational aspects of the protein, which are integrated into the final secretion prediction.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SecretomeP

:: MORE INFORMATION

Citation

Feature based prediction of non-classical and leaderless protein secretion
J. Dyrløv Bendtsen, L. Juhl Jensen, N. Blom, G. von Heijne and S. Brunak
Protein Eng. Des. Sel., 17(4):349-356, 2004

SeaView 5.0.5 – Sequence Alignment and Phylogenetic Tree Building

SeaView 5.0.5

:: DESCRIPTION

SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

 SeaView

:: MORE INFORMATION

Citation

Gouy M., Guindon S. & Gascuel O. (2010)
SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building.
Molecular Biology and Evolution 27(2):221-224.

ArgusLab 4.0.1 – Molecular Modeling, Graphics & Drug Design Program

ArgusLab 4.0.1

:: DESCRIPTION

ArgusLab is a molecular modeling, graphics, and drug design program.The ArgusDock docking engine, implemented in ArgusLab4.0, approximates an exhaustive search method, with similarities to DOCK and Glide. Flexible ligand docking is possible with ArgusLab, where the ligand is described as a torsion tree and grids are constructed that overlay the binding site. Ligand’s root node (group of bonded atoms that do not have rotatable bonds) is placed on a search point in the binding site and a set of diverse and energetically favorable rotations is created. For each rotation, torsions in breadth-first order are constructed and those poses that survive the torsion search are scored. The N-lowest energy poses are retained and the final set of poses undergoes coarse minimization, re-clustering and ranking.

::DEVELOPER

Mark A. ThompsonPlanaria Software LLC, Seattle, WA

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

ArgusLab

:: MORE INFORMATION

Citation

Thompson, M. A. (2004).
Molecular docking using ArgusLab, an efficient shape-based search algorithm and the AScore scoring function.
ACS meeting, Philadelphia, 172, CINF 42, PA.

Gromita 4.6 – GUI for GROMACS

Gromita 4.6

:: DESCRIPTION

Gromita is a Graphical User Interface (GUI) for GROMACS (v.3 and 4). It is writen in perl making extensive use of perl/tk achieving portability in a wide variety of operating systems and architectures. Gromita provides friendly to use buttons in a windows-based environment while maintaining a terminal mode for the experienced user.

::DEVELOPER

Gromita Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Gromita

:: MORE INFORMATION

Citation

Sellis D, Vlachakis D, Vlassi M. (2009)
Gromita: A Fully Integrated Graphical User Interface to Gromacs 4.
Bioinform Biol Insights 2009:3 99-102

Desmond 2023.2 – High-speed Molecular Dynamics Simulation

Desmond 2023.2

:: DESCRIPTION

Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer.

::DEVELOPER

D. E. Shaw Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Window / Linux / Mac OsX
  • Python

:: DOWNLOAD

Desmond

:: MORE INFORMATION

Citation

Kevin J. Bowers, Edmond Chow, Huafeng Xu, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, Mark A. Moraes, Federico D. Sacerdoti, John K. Salmon, Yibing Shan, and David E. Shaw,
Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters,”
Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, November 11–17, 2006

CoPlot 6.45 – Software for Great Scientific Graphs, Maps, and Technical Drawings

CoPlot 6.45

:: DESCRIPTION

CoPlot is an incredibly versatile program for making publication-quality 2D and 3D scientific graphs (which plot data and equations), maps, and technical drawings. Every aspect of CoPlot has been designed around one basic goal: to make a program that is so versatile that scientists and engineers can easily get exactly what they want. CoPlot includes CoStat for data handling and statistics.

::DEVELOPER

CoHort Software

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java

:: DOWNLOAD

CoPlot

:: MORE INFORMATION

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