Tag: Diversity

CoDiDi – Correlation between Diversity and Diferentiation

CoDiDi

:: DESCRIPTION

CoDiDi is program for estimating Gst, Hs and their correlation coefficient from marker data. It can be used to detect the presence or absence of mutational effect on the marker based genetic differentiation statistic Gst.

:: DEVELOPER

Dr Jinliang Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CoDiDi

:: MORE INFORMATION

Citation

Wang J.
Does GST underestimate genetic differentiation from marker data?
Mol Ecol. 2015 Jul;24(14):3546-58. doi: 10.1111/mec.13204. Epub 2015 May 14. PMID: 25891752.

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 Meiosis , Snurfle Meiosis and Genetics 2 

:: MORE INFORMATION

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.

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.

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.

MACiE 3.0 – Exploring the Diversity of Biochemical Reactions

MACiE 3.0

:: DESCRIPTION

MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of fully annotated enzyme reaction mechanisms.

::DEVELOPER

Thornton group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MACiE: exploring the diversity of biochemical reactions.
Holliday GL, Andreini C, Fischer JD, Rahman SA, Almonacid DE, Williams ST, Pearson WR.
Nucleic Acids Res. 2012 Jan;40(Database issue):D783-9.