TIGER 1.2.0-beta – Toolbox for Integrating Genome-scale metabolism, Expression, and Regulation

TIGER 1.2.0-beta

:: DESCRIPTION

TIGER is a software platform for building and analyzing genome-scale models of metabolism. TIGER provides methods for combining gene-protein-reaction associations, transcriptional regulation, and other biological constraints into a single mixed-integer linear programming (MILP) framework.

::DEVELOPER

the Computational Systems Biology Laboratory, Department of Biomedical Engineering, University of Virginia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Matlab

:: DOWNLOAD

TIGER

:: MORE INFORMATION

Citation

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks.
Jensen PA, Lutz KA, Papin JA.
BMC Syst Biol. 2011 Sep 23;5:147. doi: 10.1186/1752-0509-5-147.

TIGER 1.02 – Identify Rapidly-evolving Characters in Evolutionary Data

TIGER 1.02

:: DESCRIPTION

TIGER is open source software for identifying rapidly evolving sites (columns in an alignment, or characters in a morphological dataset). It can deal with many kinds of data (molecular, morphological etc.). Sites like these are important to identify as they are very often removed or reweighted in order to improve phylogenetic reconstruction. When a site is changing very quickly between taxa it might not hold much phylogenetic information and therefore might simply be a source of noise. Use of TIGER can (a) allow you to see the amount of rapid evolution and noise in your alignment and (b) provide a quick and easy way to remove as many of the “noisy” sites as possible.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOS
Python

:: DOWNLOAD

TIGER

:: MORE INFORMATION

Citation:

Cummins, C.A. and McInerney, J.O. (2011)
A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases.
Systematic Biology 60 (6) 833-844.

TIGER – DNA Sequence Assembly

TIGER

:: DESCRIPTION

Tiger is a novel de novo assembly framework which adapts to available computing resources by iteratively decomposing the assembly problem into sub-problems.

::DEVELOPER

IMPACT Reach Group (Illinois Microarchitecture Project using Algorithms and Compiler Technology)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

TIGER

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 19:S18. doi: 10.1186/1471-2105-13-S19-S18. Epub 2012 Dec 19.
TIGER: tiled iterative genome assembler.
Wu XL1, Heo Y, El Hajj I, Hwu WM, Chen D, Ma J.