Tag: CGAT

CGAT – Comparative Genome Analysis Tool

CGAT

:: DESCRIPTION

CGAT is a Comparative Genome Analysis Tool that was depeloped for detailed comparison of closely related bacterial-sized genomes. CGAT visualizes precomputed pairwise genome alignments on both dotplot and alignment viewers. Users can put several information on this alignment, such as existence of tandem repeats or interspersed repetitive sequences and changes in codon usage bias, to facilitate interpretation of the observed genomic changes.

::DEVELOPER

Ikuo Uchiyama (uchiyama@nibb.ac.jp)

:: SCREENSHOTS

cgta

:: REQUIREMENTS

  •  Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 CGAT

:: MORE INFORMATION

Citation

CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes.
Uchiyama I, Higuchi T, Kobayashi I.
BMC Bioinformatics. 2006 Oct 24;7:472.

CGAT Apps 0.4.0 – Scripts for Genomics and Next-generation Sequencing Analysis

CGAT Apps 0.4.0

:: DESCRIPTION

The CGAT App contains scripts and pipelines developed by CGAT. The collection contains scripts for genomics and next-generation sequencing analysis, but also general purpose scripts.

::DEVELOPER

Computational Genomics: Analysis and Training (GCAT)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

CGAT Apps

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 May 1;30(9):1290-1. doi: 10.1093/bioinformatics/btt756. Epub 2014 Jan 5.
CGAT: computational genomics analysis toolkit.
Sims D1, Ilott NE, Sansom SN, Sudbery IM, Johnson JS, Fawcett KA, Berlanga-Taylor AJ, Luna-Valero S, Ponting CP, Heger A.