Tag: Metagenomic Sequences

PhylOTU – Phylogenetic Clustering of Metagenomic Sequences into OTUs

PhylOTU

:: DESCRIPTION

PhylOTU identifies microbial operational taxonomic units (OTUs) from metagenomic data.

::DEVELOPER

Pollard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl
  • BIoPerl
  • C++ COmpiler

:: DOWNLOAD

 PhylOTU

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2011 Jan 20;7(1):e1001061. doi: 10.1371/journal.pcbi.1001061.
PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.
Sharpton TJ1, Riesenfeld SJ, Kembel SW, Ladau J, O’Dwyer JP, Green JL, Eisen JA, Pollard KS.

CLaMS / iClaMS – Classifier for Metagenomic Sequences

CLaMS / iClaMS

:: DESCRIPTION

ClaMS is a metagenome binning/clustering tool. It bins sequences to user-defined training sets by comparing signatures computed from their composition.

iClaMS consists of a Perl wrapper script that separates a sequence set into bins by training on the sequence set itself. Directions for running both ClaMS and iClaMS are included in the README in the tar archive.

::DEVELOPER

DOE Joint Genome Institute

:: SCREENSHOTS

ClaMS

::REQUIREMENTS

  • Linux / MacOsX /Windows
  • Java

:: DOWNLOAD

 CLaMS / iClaMS

:: MORE INFORMATION

Citation

ClaMS: A Classifier for Metagenomic Sequences.
Pati A, Heath LS, Kyrpides NC, Ivanova N.
Stand Genomic Sci. 2011 Nov 30;5(2):248-53. doi: 10.4056/sigs.2075298. Epub 2011 Nov 28.