Tag: Phenotyping

ScanAFLP 1-3 – Evaluate AFLP Electropherograms for Phenotyping and Marker selection

ScanAFLP 1-3

:: DESCRIPTION

ScanAFLP : a R script to evaluate AFLP electropherograms for phenotyping and marker selection based on peak height distribution and repeatability using blind controls.

::DEVELOPER

Laboratoire d’Ecologie Alpine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ScanAFLP

:: MORE INFORMATION

Citation

Herrmann D., Poncet B. N., Manel S., Rioux D., Gielly L., Taberlet P., Gugerli F (2010)
Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates.
Molecular Ecology 53:302-310.

P-TRAP – Panicle Trait Phenotyping tool

P-TRAP

:: DESCRIPTION

P-TRAP (Panicle TRAits Phenotyping), is a free and new open source software that automatically recognizes, from numeric images, the structure of a panicle and the seeds on the panicle. The software processes and quantifies several traits related to the structures of the panicles, detects and counts the grains, and measures their shape parameters. P-TRAP offers both efficient results and friendly environment for users to perform their experiments. Comparing to the data obtained by manual processing, P-TRAP produces reliable results in much lesser time. Furthermore, manual processing is not repeatable because dry panicles are vulnerable to damage. The software is very useful, practical and collects much more data than human operators.

::DEVELOPER

The IRD bioinformatics

:: SCREENSHOTS

P-TRAP

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 P-TRAP

:: MORE INFORMATION

Citation

BMC Plant Biol. 2013 Aug 29;13:122. doi: 10.1186/1471-2229-13-122.
P-TRAP: a Panicle Trait Phenotyping tool.
Al-Tam F, Adam H, Anjos AD, Lorieux M, Larmande P, Ghesquière A, Jouannic S, Shahbazkia HR.

IrisPlex and HIrisPlex Eye and Hair Colour DNA Phenotyping Webtool

IrisPlex and HIrisPlex Eye and Hair Colour DNA Phenotyping Webtool

:: DESCRIPTION

IrisPlex and HIrisPlex Eye and Hair Colour DNA Phenotyping Webtool allows obtaining eye and hair colour phenotypes from full or partial IrisPlex and HIrisPlex DNA genotypes using large underlying genotype and phenotype databases we previously developed and published.

::DEVELOPER

Dept Genetic Identification ErasmusMC Rotterdam

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA.
Walsh S, Liu F, Wollstein A, Kovatsi L, Ralf A, Kosiniak-Kamysz A, Branicki W, Kayser M.
Forensic Sci Int Genet. 2013 Jan;7(1):98-115. doi: 10.1016/j.fsigen.2012.07.005

PhenoTips 1.4.7 – Patient Phenotyping software

PhenoTips 1.4.7

:: DESCRIPTION

PhenoTips is an open source software tool for collecting and analyzing phenotypic information for patients with genetic disorders.

::DEVELOPER

Computational Biology Lab at the University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PhenoTips

:: MORE INFORMATION

Citation:

Hum Mutat. 2013 Aug;34(8):1057-65. doi: 10.1002/humu.22347. Epub 2013 May 24.
PhenoTips: patient phenotyping software for clinical and research use.
Girdea M1, Dumitriu S, Fiume M, Bowdin S, Boycott KM, Chénier S, Chitayat D, Faghfoury H, Meyn MS, Ray PN, So J, Stavropoulos DJ, Brudno M.

HTPheno – Image Analysis Pipeline for High-Throughput Phenotyping

HTPheno

:: DESCRIPTION

HTPheno is a software for high-throughput plant phenotyping is presented. HTPheno is implemented as a plugin for ImageJ, an open source image processing software. It provides the possibility to analyse colour images of plants which are taken in two different views (top view and side view) during a screening. Within the analysis different phenotypical parameters for each plant such as height, width and projected shoot area of the plants are calculated for the duration of the screening.

::DEVELOPER

HTPheno Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 HTPheno

:: MORE INFORMATION

Citation

A. Hartmann, T. Czauderna, R. Hoffmann, N. Stein and F. Schreiber.
HTPheno: An Image Analysis Pipeline for High-Throughput Plant Phenotyping.
BMC Bioinformatics, 12:e148, 2011.