Tag: CAT

CAT/BAT v5.2.3 – Taxonomic Classification of Contigs and Metagenome-assembled Genomes

CAT/BAT v5.2.3

:: DESCRIPTION

Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies.

::DEVELOPER

Bas E. Dutilh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

CAT/BAT

:: MORE INFORMATION

Citation

von Meijenfeldt FAB, Arkhipova K, Cambuy DD, Coutinho FH, Dutilh BE.
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT.
Genome Biol. 2019 Oct 22;20(1):217. doi: 10.1186/s13059-019-1817-x. PMID: 31640809; PMCID: PMC6805573.

CAT / Xat 0.8.6 – Cross-species Alignment Tool

CAT / Xat 0.8.6

:: DESCRIPTION

 CAT (Xat) is designed to be a cross-species (both intra-species and inter-species), nucleotide level, cDNA-to-genome alignment software. It uses improved heuristics to effectively balance specificity, sensitivity and speed, and is optimized for genome-wide mapping.

::DEVELOPER

CAT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 CAT / Xat

:: MORE INFORMATION

Citation

A cross-species alignment tool (CAT).
Li H, Guan L, Liu T, Guo Y, Zheng WM, Wong GK, Wang J.
BMC Bioinformatics. 2007 Sep 19;8:349.

CAT 1.3 – Composition Analysis Toolkit

CAT 1.3

:: DESCRIPTION

CAT (Composition Analysis Toolkit) is a software package that includes a novel measure of codon usage bias, Codon Deviation Coefficient (CDC). Unlike previous measures, CDC effectively accounts for background nucleotide composition in estimating codon usage bias and utilizes a bootstrap assessment of the statistical significance of codon usage bias.

::DEVELOPER

The National Genomics Data Center (NGDC)

:: SCREENSHOTS

:: REQUIREMENTS

  • WIndows/ Linux / MacOsX

:: DOWNLOAD

 CAT

:: MORE INFORMATION

Citation

Zhang, Z., Li, J., Cui, P., Ding, F., Li, A., Townsend, J.P., and Yu, J. (2011)
Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance
BMC Bioinformatics. 2012 Mar 22;13:43.