HoloVir 1.0 – Investigating the Diversity and Function of Viruses in Invertebrate Holobionts

HoloVir 1.0

:: DESCRIPTION

HoloVir is a robust and flexible data analysis pipeline that provides an optimised and validated workflow for taxonomic and functional characterisation of viral metagenomes.

::DEVELOPER

CUBE – Bioinformatics and Computational Systems Biology, University of Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

HoloVir

:: MORE INFORMATION

Citation:

Front Microbiol, 7, 822 2016 Jun 9 eCollection 2016
HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts
Patrick W Laffy et al.

CRISPRmap 2.1- CRISPR Repeat Conservation and Diversity Analysis

CRISPRmap 2.1

:: DESCRIPTION

CRISPRmap provides a quick and detailed insight into repeat conservation and diversity of both bacterial and archaeal systems. It comprises the largest dataset of CRISPRs to date and enables comprehensive independent clustering analyses to determine conserved sequence families, potential structure motifs for endoribonucleases, and evolutionary relationships.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci.
Alkhnbashi OS, Costa F, Shah SA, Garrett RA, Saunders SJ, Backofen R.
Bioinformatics. 2014 Sep 1;30(17):i489-i496. doi: 10.1093/bioinformatics/btu459.

Nucleic Acids Res. 2013 Sep;41(17):8034-44. doi: 10.1093/nar/gkt606. Epub 2013 Jul 17.
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems.
Lange SJ1, Alkhnbashi OS, Rose D, Will S, Backofen R.

DIVEIN – Analyze Phylogenies, Sequence Divergence, Diversity and Informative Sites

DIVEIN

:: DESCRIPTION

DIVEIN is a web service that performs automated maximum likelihood phylogenetic analyses of nucleotide and amino acid sequences. Starting with a set of aligned sequences

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Biotechniques. 2010 May;48(5):405-8. doi: 10.2144/000113370.
DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites.
Deng W1, Maust BS, Nickle DC, Learn GH, Liu Y, Heath L, Kosakovsky Pond SL, Mullins JI.

DARwin 6.0.010 – Diversity and Phylogenetic Analysis

DARwin 6.0.010

:: 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.

Dover Analyzer 0.1.2 – Overlap and Diversity in Antimicrobial Peptide Database

Dover Analyzer 0.1.2

:: DESCRIPTION

Dover Analyzer is a wizard like application that takes collections of databases annotated in FASTA format and guides the user through a few steps to compute the overlap, diversity and redundant or non-redundant sets of peptide sequences.

::DEVELOPER

Molecular Biosilico Discovery MultiSystem

:: SCREENSHOTS

DoverAnalyzer

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 Dover Analyzer

:: MORE INFORMATION

Citation

Overlap and diversity in antimicrobial peptide databases: compiling a non-redundant set of sequences.
Aguilera-Mendoza L, Marrero-Ponce Y, Tellez-Ibarra R, Llorente-Quesada MT, Salgado J, Barigye SJ, Liu J.
Bioinformatics. 2015 Mar 29. pii: btv180.

Contrib 1.4 – Contribution of Each Population to Total Diversity

Contrib 1.4

:: DESCRIPTION

Contrib providse a measure of the contribution of each population to total diversity (measured by H, the expected heterozygosity, or by R, the allelic richness). This contribution is splitted in two components: one due to the
diversity of the population, the other due to its differentiation from the remaining populations.

::DEVELOPER

Rémy Petit (Petit@pierroton.inra.fr), INRA-Bordeaux

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Contrib

:: MORE INFORMATION

Citation

Petit, El Mousadik & Pons. 1998.
Identifying populations for conservation on the basis of genetic markers.
Conservation Biology 12, 844-855.

Aflpdiv 1.1 – Compute Comparable Measures of Diversity from AFLP Data

Aflpdiv 1.1

:: DESCRIPTION

Aflpdiv computes comparable measures of diversity (allelic richness and % polymorphic loci) from AFLP data.

::DEVELOPER

Rémy Petit (Petit@pierroton.inra.fr), INRA-Bordeaux

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Aflpdiv

:: MORE INFORMATION

Citation

Coart E, Van Glabeke S, Petit RJ, Van Bockstaele E, Roldan-Ruiz I:
Range wide versus local patterns of genetic diversity in hornbeam (Carpinus betulus L.).
Conservation Genetics 2005, 6:259-273

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

PermutCpSSR 1.2.1 – Measures of Diversity and Differenciation from Haploid Population Genetic data

PermutCpSSR 1.2.1

:: DESCRIPTION

PERMUT computes measures of diversity and differenciation from haploid population genetic data, when a measure of the distance between haplotypes is available,and test whether the differentiation and diversity measures differ from the equivalent measures that do not take into account the distances between haplotypes

CpSSR computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered

::DEVELOPER

Rémy Petit (Petit@pierroton.inra.fr), INRA-Bordeaux

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 PermutCpSSR

:: MORE INFORMATION

Citation

Mol Ecol. 1999 Oct;8(10):1593-602.
Rangewide variation of the maritime pine bast scale matsucoccus feytaudi duc. (Homoptera: matsucoccidae) in relation to the genetic structure of its host
Burban C, Petit RJ, Carcreff E, Jactel H.