GENtle2 0.7.0 – Web-Based DNA Editor for Synthetic Biology

GENtle2 0.7.0

:: DESCRIPTION

GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more.

::DEVELOPER

Synbiota Inc.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

  GENtle

:: MORE INFORMATION

TreesimJ 0.7 – Population Genetics Simulator Program

TreesimJ 0.7

:: DESCRIPTION

TreesimJ is a flexible, individual-based population genetic simulator. It tracks the state of a population evolving in forward time via discrete, Wright-Fisher generations.   It also maintains the full genealogical tree of the population and allows for collecting sample trees which can be analyzed, exported and logged.  It can also simulate evolving DNA under a variety of assumptions regarding mutation and selection. TreesimJ is very flexible, meaning that a wide variety of fitness models, demographic models, and data collectors are supported, and new models are easy to write.  The application also sports an intuitive graphical interface, so users unfamiliar with the command line or XML can easily use the program to generate and analyze genetic data.

::DEVELOPER

Brendan O’Fallon

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

TreesimJ

:: MORE INFORMATION

Citation:

Brendan O’Fallon
TreesimJ: a flexible, forward time population genetic simulator
Bioinformatics (2010) 26 (17): 2200-2201

Genepop 4.5 – Population Genetics Software Package

Genepop 4.5

:: DESCRIPTION

GENEPOP is a population genetics software package

::DEVELOPER

Michel Raymond (Raymond@isem.univ-montp2.fr) and Francois Rousset (Rousset@isem.univ-montp2.fr)

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux  / Windows

:: DOWNLOAD

 Genepop

:: MORE INFORMATION

Citation

Rousset, F., 2008.
Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux.
Mol. Ecol. Resources 8: 103-106.

MEGA 7 Beta – Molecular Evolutionary Genetics Analysis

MEGA 7 Beta

:: 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

visPIG 1.1 – Visual Plotting Interface for Genetics

visPIG 1.1

:: DESCRIPTION

visPIG is a web application to produce multi-track, multi-scale, multi-region plots of genetic data.

::DEVELOPER

Marc Henrion

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ MacOsX/Linux
  • R

:: DOWNLOAD

  visPIG

:: MORE INFORMATION

Citation:

visPIG–a web tool for producing multi-region, multi-track, multi-scale plots of genetic data.
Scales M, Jäger R, Migliorini G, Houlston RS, Henrion MY.
PLoS One. 2014 Sep 10;9(9):e107497. doi: 10.1371/journal.pone.0107497. eCollection 2014.

GGtools 5.4.0 – Analysis of Genetics of Gene Expression

GGtools 5.4.0

:: DESCRIPTION

GGtools is a software and data for analyses in genetics of gene expression and/or DNA methylation

:: DEVELOPER

Vincent J Carey

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

 GGtools

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Feb 15;23(4):522-3. Epub 2006 Dec 8.
GGtools: analysis of genetics of gene expression in bioconductor.
Carey VJ, Morgan M, Falcon S, Lazarus R, Gentleman R.

Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x.
Carey VJ, Davis AR, Lawrence MF, Gentleman R, Raby BA.
Bioinformatics. 2009 Jun 1;25(11):1447-8. doi: 10.1093/bioinformatics/btp169.

Snurfle Meiosis 1.1 / Snurfle Meiosis and Genetics 2 – Diversity and Dihybrid Crosses

Snurfle Meiosis 1.1 / Snurfle Meiosis and Genetics 2

:: DESCRIPTION

Snurfle Meiosis : Snurfles, just like any other organism, must reproduce in order to continue as a species! But how does this happen? By the end of this game, you will understand how MEIOSIS and FERTILIZATION work to make offspring! You will also see how GENETIC characteristics are passed on through these processes and the connection between meiosis and genetics!

Snurfle Meiosis and Genetics 2 : When Snurfles reproduce, their offspring can have a lot of different traits (lots of diversity). But how?  By the end of this game, you will understand how the processes of CROSSING OVER, INDEPENDENT ASSORTMENT, and RANDOM FERTILIZATION result in increased diversity of offspring!  Also, you will learn how to perform a DIHYBRID CROSS!

::DEVELOPER

BioMan Biology

:: SCREENSHOTS

SnurfleMeiosis

:: REQUIREMENTS

  • Web browser / iPad/ iPhone

:: DOWNLOAD

 Snurfle MeiosisSnurfle Meiosis and Genetics 2 

:: MORE INFORMATION

Genetix 4.05 – Set of Population Genetics Programs

Genetix 4.05

:: DESCRIPTION

Genetix is a set of programs which computes several basic parameters of population genetics such as Nei’s D and H, Wright’s F-statistics (the Weir-Cockerham’s and Robertson-Hill’s estimators), and linkage disequilibrium D according to Black & Krafsur. For each of them, the distribution of the parameter values under the null hypothesis (for instance Hardy-Weinberg equilibrium for Fstats) is generated by the appropriate resampling scheme of the relevant objects (e.g. alleles between individuals in the case of Fis) using permutations.

::DEVELOPER

Khalid Belkhir

:: SCREENSHOTS

Genetix

::REQUIREMENTS

  • Windows

:: DOWNLOAD

 Genetix

:: MORE INFORMATION

Hands On Genetics 2.6 – Interactive Education Programs of Genetics

Hands On Genetics 2.6

:: DESCRIPTION

Hands On Genetics is a suite of interactive programs covering a wide range of topics in genetics.
Mendelian genetics:
SimpleGene, Mendelsim, SexLink, Punnett, GeneShare

Cytogenetics:
Meiosis

Molecular genetics:
Genetic molecules, PCR, Gelsim

Population genetics:
Popsim, Hardy-Weinberg, Fisher-Wright

::DEVELOPER

Hands On Genetics Editorial Board

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOSX

:: DOWNLOAD

Hands On Genetics

:: MORE INFORMATION

Bugsville 1.0 – Simulates the Genetics of a Quantitative Character

Bugsville 1.0

:: DESCRIPTION

Bugsville simulates the genetics of a quantitative character. The user can breed ladybugs to estimate the heritability of spot number, then conduct a selective breeding experiment to see if the heritability multiplied by the selection differential predicts the response to selection.

::DEVELOPER

Jon C. Herron

:: SCREENSHOTS

Bugsville

:: REQUIREMENTS

  • MacOsX / Windows

:: DOWNLOAD

 Bugsville

:: MORE INFORMATION