Tag: Molecular Biology

MBEToolbox 3.0 – MATLAB Molecular Biology & Evolution Toolbox

MBEToolbox 3.0

:: DESCRIPTION

MBEToolbox is a tool which aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned Matlab users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution.

::DEVELOPER

Cai Laborary

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MBEToolbox

:: MORE INFORMATION

Citation:

James J Cai, David K Smith, Xuhua Xia, Kwok-yung Yuen.
MBEToolbox 2.0: An enhanced version of a MATLAB toolbox for Molecular Biology and Evolution
Evolutionary Bioinformatics Online 2006, 2 189-192

DAMBE 5.3.48 – Sequence Data Analysis in Molecular Biology and Evolution

DAMBE 5.3.48

:: DESCRIPTION

DAMBE (data analysis in molecular biology and evolution) is an integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data.

::DEVELOPER

Dr. Xuhua Xia

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

DAMBE

:: MORE INFORMATION

Citation:

Xia, X. 2013.
DAMBE5: A comprehensive software package for data analysis in molecular biology and evolution.
Molecular Biology and Evolution 30:1720-1728

Xia, X., and Xie. Z., 2001
DAMBE: Data analysis in molecular biology and evolution.
Journal of Heredity 92:371-373.

Genome Projector – Zoomable User Interface for Molecular Biology

Genome Projector

:: DESCRIPTION

Genome Projector, a searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk.

::DEVELOPER

GenomeProjector Team

:: SCREENSHOTS

GenomeProjector

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Genome Projector: zoomable genome map with multiple views.
Arakawa K, Tamaki S, Kono N, Kido N, Ikegami K, Ogawa R, Tomita M.
BMC Bioinformatics. 2009 Jan 23;10:31. doi: 10.1186/1471-2105-10-31.

BioGranat 0.1 – Molecular Biology Graph Visualisation and Analysis Tool

BioGranat 0.1

:: DESCRIPTION

BioGranat is a molecular biology graph visualisation and analysis tool. It is based on the Java OSGi bundle architecture and currently provides a graphical user interface, input and output routines for various graph file formats, a facility to use the JUNG library, 2D graph layout routines, 3D visualisation of graphs, JAVA scripting and graph analysis algorithms.

:: DEVELOPER

Hochschule Hannover and King’s College London

:: SCREENSHOTS

BioGranat

:: REQUIREMENTS

  • Windows
  • Java

:: DOWNLOAD

 BioGranat

:: MORE INFORMATION

Citation

Dand N, Sprengel F, Ahlers V, Schlitt T
BioGranat-IG: A network analysis tool to suggest mechanisms of genetic heterogeneity from exome sequencing data
Bioinformatics. 2013,29(6):733-741.

ABNER 1.5 – Molecular Biology Text Analysis

ABNER 1.5

:: DESCRIPTION

ABNER (A Biomedical Named Entity Recognizer) is a software tool for molecular biology text analysis.

::DEVELOPER

Burr Settles

:: SCREENSHOTS

:: REQUIREMENTS

  •  Windows /Linux/MacOsX
  • Java

:: DOWNLOAD

  ABNER

:: MORE INFORMATION

Citation

B. Settles (2005).
ABNER: an open source tool for automatically tagging genes, proteins, and other entity names in text.
Bioinformatics, 21(14):3191-3192., 2005.

Aipotu 1.3.2 – Simulation Linking Genetics, Biochemistry, Molecular Biology & Evolution

Aipotu 1.3.2

:: DESCRIPTION

Aipotu creates a utopia that simulates the genetics, biochemistry, molecular biology, and evolution of organisms in a biologically reasonable and pedagogically relevant way.

::DEVELOPER

Brian White

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

Aipotu

:: MORE INFORMATION

Virtlab 1.3 – Simulate Molecular Biology Laboratory

Virtlab 1.3

:: DESCRIPTION

VIRTLAB is a self-training program based on PBL (Problem-Based- Learning Pathway) built to simulate a molecular biology laboratory. It has been designed to stimulate students in the biological sciences to analyse and solve molecular biology problems using standard laboratory techniques (e.g. restriction enzyme digestions, analytical and preparative agarose gels, DNA cloning and sequencing, etc.) and can thus be viewed as a teaching aid.

::DEVELOPER

G Iazzetti, G Santini, M Rau, E Bucci and R A Calogero

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Virtlab

:: MORE INFORMATION

Citation

Iazzetti G., Santini G., Rau M., Bucci E., Calogero R. A.
VIRTLAB: a virtual molecular biology laboratory.
Bioinformatics, vol.14 n.9 pp:815-816 (1998)

Molecular Basis of Medicine – Introduction to Molecular Biology

Molecular Basis of Medicine

:: DESCRIPTION

Molecular Basis of Medicine is primarily aimed at medical students without ‘A’-level Biology, but is also suitable for students in Biochemistry and related subjects. It may also be suitable as an introduction to gene expression for any students. The content consists of an introduction to cell structure (with diagrams and electron micrographs); an introduction to proteins, lipids and nucleic acids; DNA replication, transcription and translation (illustrated with animations of these processes).

::DEVELOPER

Andy Relf and Fergus Doherty

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOSX

:: DOWNLOAD

Molecular Basis of Medicine for win , for Mac

:: MORE INFORMATION