ClanTox – A Classifier of Animal Toxins

ClanTox

:: DESCRIPTION

ClanTox is a classifier of animal toxins. Given a sequence, it predicts whether the sequence is a toxin or toxin-like protein.

::DEVELOPER

ClanTox team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):i482-8. doi: 10.1093/bioinformatics/btq375.
A predictor for toxin-like proteins exposes cell modulator candidates within viral genomes.
Naamati G1, Askenazi M, Linial M.

TASSEL 5.0 / rTASSEL 0.9.23 – Association And Diversity Analyses In Plants And Animals

TASSEL 5.0 / rTASSEL 0.9.23

:: DESCRIPTION

TASSEL (Trait Analysis by aSSociation, Evolution, and Linkage) is a software package which performs a variety of genetic analyses. The analyses include association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information.

rTASSEL  construct an R-based front-end to connect to a variety of highly used TASSEL methods and analytical tools.

::DEVELOPER

The Buckler Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
  • / R

:: DOWNLOAD

 TASSEL / rTASSEL

:: MORE INFORMATION

Citation

Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007)
TASSEL: Software for association mapping of complex traits in diverse samples.
Bioinformatics 23:2633-2635.

Spatial 1.0.0 – Model Animal Movement on Landscapes

Spatial 1.0.0

:: DESCRIPTION

Spatial is an agent-based model of the movements of animals on landscapes. The landscapes can be entered from image files or from tables of data. Rules are entered to describe the attractiveness, permeability, and rate of movement of animals for each landscape feature (optionally including other animals). Spatial then simulates the movements over time, and dsiplays final location, tracks, or density of occupancy.

::DEVELOPER

The SCTI Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Spatial 

:: MORE INFORMATION

TreeFam r9 – Database of Animal Gene Trees

TreeFam r9

:: DESCRIPTION

TreeFam is a database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.

::DEVELOPER

TreeFam team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

TreeFam v9: a new website, more species and orthology-on-the-fly.
Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A.
Nucleic Acids Res. 2013 Nov 4

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D572-80.
TreeFam: a curated database of phylogenetic trees of animal gene families.
Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin R.

ImagePlane – Analysis of Images of the Animal S. Mediterranea

ImagePlane

:: DESCRIPTION

ImagePlane is python based image analysis software designed for the automated analysis of images of the animal S. mediterranea. This software allows the animals’s neoblasts to be quantified and tested for assymetries along its veritcal and hoizontal axes. ImagePlane also allows simple mophology categorizations to be made based on the overall shape of the animal.

::DEVELOPER

Yandell Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler
  • Python

:: DOWNLOAD

  ImagePlane

:: MORE INFORMATION