BioMercator v4.2.3 – Genetic Maps and QTL Integration

BioMercator v4.2.3

:: DESCRIPTION

BioMercator is a standalone application for: (1) Displaying genetic maps and QTL through a graphical user interface. (2) Performing automatic compilations of several genetic maps through a projection process. (3) Computing meta-analysis of QTL detected in independent experiments.

:: DEVELOPER

ABI Bioinformatic and Informatic Team 

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 BioMercator

:: MORE INFORMATION

Citation:

Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J.
BioMercator: integrating genetic maps and QTL towards discovery of candidate genes.
Bioinformatics. (2004) Sep 22;20(14):2321-6.

Olivier Sosnowski, Alain Charcosset and Johann Joets.
 BioMercator V3: an upgrade of genetic map compilation and QTL meta-analysis algorithms
Bioinformatics. 2012 Aug 1;28(15):2082-3. doi: 10.1093/bioinformatics/bts313.

MEGA 12.1 – Molecular Evolutionary Genetics Analysis

MEGA 12.1

:: DESCRIPTION

MEGA （Molecular Evolutionary Genetics Analysis）is an integrated tool for automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.

::DEVELOPER

MEGA Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

MEGA

:: MORE INFORMATION

Citation

Mol Biol Evol. 2013 Dec;30(12):2725-9. doi: 10.1093/molbev/mst197. Epub 2013 Oct 16.
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011)
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods.
Molecular Biology and Evolution (2011)doi: 10.1093/molbev/msr121 First published online: May 4, 2011

DARwin 6.0.021 – Diversity and Phylogenetic Analysis

DARwin 6.0.021

:: DESCRIPTION

DARwin (Dissimilarity Analysis and Representation for Windows) is a software package developed for diversity and phylogenetic analysis on the basis of evolutionary dissimilarities.

::DEVELOPER

DARwin Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 DARwin

:: MORE INFORMATION

Citation:

Perrier, X., Flori, A. , Bonnot, F. (2003). Data analysis methods.
In: Hamon, P., Seguin, M., Perrier, X. ,Glaszmann, J. C. Ed., Genetic diversity of cultivated tropical plants. Enfield, Science Publishers. Montpellier. pp 43 – 76.

HyperTree 1.2.2 – Java Phylogenetic Tree Viewer

HyperTree 1.2.2

:: DESCRIPTION

HYPERTREE is a Java phylogenetic tree viewer, with a hyperbolic (‘fish-eye’) view and editing abilities that help in managing very large trees.

::DEVELOPER

kinase.com

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

 HyperTree

:: MORE INFORMATION

Citation

Visualizing harge hierarchical clusters in hyperbolic space
J. Bingham, S Sudarsanam
Bioinformatics (2000) 16(7): 660-1

VESTA 3.90.5a – 3D Visualization System for Electronic & Structural Analysis

VESTA 3.90.5a

:: DESCRIPTION

VESTA (Visualization System for Electronic & Structural Analysis) is a 3D visualization program for structural models and 3D grid data such as electron/nuclear densities. Some of the novel features of VESTA are listed below.

::DEVELOPER

Koichi Momma

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 VESTA

:: MORE INFORMATION

Citation

K. Momma and F. Izumi,
“VESTA: a three-dimensional visualization system for electronic and structural analysis,”
J. Appl. Crystallogr., 41:653-658, 2008.

PhyloBayes 4.1c – Bayesian Phylogenetic software based on Mixture Models

PhyloBayes 4.1c

:: DESCRIPTION

PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. Compared to other phylogenetic MCMC samplers (e.g. MrBayes), the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT. It is particularly well suited for large multigene alignments, such as those used in phylogenomics.

::DEVELOPER

Nicolas Lartillot (nicolas.lartillot@umontreal.ca)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

 PhyloBayes

:: MORE INFORMATION

Citation

Nicolas Lartillot, Thomas Lepage and Samuel Blanquart
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
Bioinformatics (2009) 25 (17): 2286-2288.

ACD/NMR Processor Academic Edition 12 – Free NMR processing software

ACD/NMR Processor Academic Edition 12

:: DESCRIPTION

ACD/NMR Processor Academic Edition has basic and advanced functions for processing 1D and 2D NMR data from any instrument quickly and efficiently. Use ACD/NMR Processor at the instrument, or away from the lab, to carry out basic spectral manipulations, attach chemical structures and assign correlations, handle spectral series, add or subtract spectra, and much more. ACD/NMR Processor Academic Edition includes ACD/ChemSketch Freeware and all of the same processing features of ACD/NMR Processor.

::DEVELOPER

Advanced Chemistry Development

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

ACD/NMR Processor Academic Edition

:: MORE INFORMATION

ACD/NMR Processor Academic Edition is for academic and non-commercial use only.

AutoDock Vina 1.2.7 – Molecular Docking and Virtual Screening Program

AutoDock Vina 1.2.7

:: 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

QMSIM 2.0 – Qtl and Marker SIMulator

QMSIM 2.0

:: DESCRIPTION

QMSim (Qtl and Marker SIMulator) was designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data.

::DEVELOPER

Mehdi Sargolzaei , Flavio Schenkel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 QMSim

:: MORE INFORMATION

Citation

Sargolzaei, M. and F. S. Schenkel. 2009.
QMSim: a large-scale genome simulator for livestock.
Bioinformatics, 25: 680-681. doi:10.1093 /bioinformatics/btp045

HBAT v2 – Hydrogen Bond Analysis Tool

HBAT v2

:: DESCRIPTION

HBAT (Hydrogen Bond Analysis Tool) is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. Other related tools available from HBAT Project are PDIA(Post Docking Interaction Analysis) and HBNG(Hydrogen Bond Network Graph).

::DEVELOPER

Abhishek Tiwari & Sunil Kumar Panigrahi

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

HBAT

:: MORE INFORMATION

Citation

HBAT: a complete package for analysing strong and weak hydrogen bonds in macromolecular crystal structures.
Tiwari A, Panigrahi SK.
In Silico Biol. 2007;7(6):651-61.