Endog 4.8 – Analyse Pedigree Information

Endog 4.8

:: DESCRIPTION

ENDOG‘s Primary functions are the computation of the individual inbreeding (F) (Wright, 1931) and the average relatedness (AR) (Gutiérrez et al., 2003; Goyache et al., 2003) coefficients. Additionally, users can compute with ENDOG useful parameters in population genetics such as that described for Biochard et al. (1997) for the number of ancestors explaining genetic variability or those proposed by Robertson (1953) and Vassallo et al. (1996) for the genetic importance of the herds. ENDOG also can compute F statistics (Wright, 1978) from genealogical information following Caballero and Toro (2000; 2002). Moreover, the present version of ENDOG calculates effective population size following different methodologies including regression approaches and particularly the recently proposed realized effective population size from individual increase in inbreeding (Gutiérrez et al., 2008), modified to account for avoidance of self-fertilization (Gutiérrez et al., 2009).

::DEVELOPER

Juan Pablo Gutiérrez García

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Endog

:: MORE INFORMATION

Citation

A note on ENDOG: a computer program for analysing pedigree information.
Gutiérrez JP, Goyache F.
J Anim Breed Genet. 2005 Jun;122(3):172-6.

PreMeta – Exchange of Information between four software packages for Meta-analysis

PreMeta

:: DESCRIPTION

PreMeta is a software program written in C++ that is designed to facilitate the exchange of information between four software packages for meta-analysis of rare-variant associations: MASS, RAREMETAL, MetaSKAT, and seqMeta.

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

PreMeta

:: MORE INFORMATION

Citation

Tang ZZ, Bunn P, Tao R, Liu Z, Lin DY.
PreMeta: a tool to facilitate meta-analysis of rare-variant associations.
BMC Genomics. 2017 Feb 14;18(1):160. doi: 10.1186/s12864-017-3573-1. PMID: 28196472; PMCID: PMC5310051.

BioLegend Flow Cytometry Application 1.6 – Information about Flow Cytometers and Fluorochromes

BioLegend Flow Cytometry Application 1.6

:: DESCRIPTION

BioLegend Flow Cytometry Application provides you with important information about your Flow Cytometers and Fluorochromes. Now you can use BioLegend’s Spectra Analyzer quickly and conveniently in the palm of your hand. We included an Antibody Usage Calculator and Timer to help with your experiments (Timer does not work in the background and will pause upon exiting the application).

::DEVELOPER

BioLegend

:: SCREENSHOTS

bfca

:: REQUIREMENTS

  • iPhone /  iPad

:: DOWNLOAD

 BioLegend Flow Cytometry Application

:: MORE INFORMATION

BRISK – Biology-Related Information Storage Kit

BRISK

:: DESCRIPTION

BRISK is a package of several web-based data management tools that provide a cohesive data integration and management platform. It was specifically designed to provide the architecture necessary to promote collaboration and expedite data sharing between scientists.

::DEVELOPER

Genapha

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Apache
  • MySQL

:: DOWNLOAD

   BRISK

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Sep 1;27(17):2422-5. doi: 10.1093/bioinformatics/btr389. Epub 2011 Jun 27.
BRISK–research-oriented storage kit for biology-related data.
Tan A, Tripp B, Daley D.

GWIPS-viz – Genome Wide Information on Protein Synthesis

GWIPS-viz

:: DESCRIPTION

GWIPS-viz aims to provide on-line tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique

::DEVELOPER

GWIPS-viz team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteomics. 2015 Mar 3. doi: 10.1002/pmic.201400603.
GWIPS-viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms.
Michel AM1, Ahern AM, Donohue CA, Baranov PV.

Uniprot DAT File Parser 1.1.5674 – Read Uniprot (IPI) .Dat file and Parse out the information for each entry

Uniprot DAT File Parser 1.1.5674

:: DESCRIPTION

The Uniprot DAT File Parser can read a Uniprot (IPI) .Dat file and parse out the information for each entry, creating a tab delimited text file. Uniprot .Dat files can be obtained from EBI’s FTP site.

::DEVELOPER

Biological MS Data and Software Distribution Center , Pacific Northwest National Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Microsoft NET Framework 3.5

:: DOWNLOAD

 Uniprot DAT File Parser

:: MORE INFORMATION

MetaCrop 2.0 – Browsing and Working with Information from the MetaCrop database

MetaCrop 2.0

:: DESCRIPTION

MetaCrop is an Add-on to enable browsing of the content of the handcurated Metacrop database. Users can directly load hand-layouted pathway maps or metabolic network models to use for browsing, pathway exploration, data-mapping and analysis or use them for metabolic modelling. The user can also filter the pathway for species specific information, which will be visually highlighted.

::DEVELOPER

Chair for Life Science Informatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jan;40(Database issue):D1173-7. Epub 2011 Nov 15.
MetaCrop 2.0: managing and exploring information about crop plant metabolism.
Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker BH, Klapperstück M, Scholz U, Weise S.

MitoSeek 1.3 – Extract Mitochondrial Genome information from Exome Sequencing data

MitoSeek 1.3

:: DESCRIPTION

MitoSeek is an open-source software tool to reliably and easily extract mitochondrial genome information from exome sequencing data. MitoSeek evaluates mitochondrial genome alignment quality, estimates relative mitochondrial copy numbers, and detects heteroplasmy, somatic mutation, and structural variance of the mitochondrial genome.

::DEVELOPER

Jiang (River) Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MitoSeek

:: MORE INFORMATION

Citation

Yan Guo, Jiang Li, Yu Shyr, David C. Samuels.
MitoSeek: Extracting Mitochondria Information and Performing High Throughput Mitochondria Sequencing Analysis.
Bioinformatics (2013) 29 (9): 1210-1211