67
(ix) MetaPhyler: MetaPhyler is tool for predicting the phylogenetic relationship
and employs phylogenetic marker genes as a taxonomic reference.
Accessible from http://metaphyler.cbcb.umd.edu (Liu et al. 2011).
(x) MTR: MTR performs clustering through multiple taxonomic ranks instead
of lowest common ancestor (LCA). Rather than LCA, this precedes the
reads one at a time; MTR take advantage of information shared by reads. It
can be reached on http://cs.ru.nl/gori/software/MTR.tar.gz (Gori et al.
2011).
(xi) NBC: NBC is an online database employing the naïve Bayes classification
system for classification of entire metagenomic reads to their best taxonomic match. Publicly available at http://nbc.ece.drexel.edu (Rosen et al.
2011).
(xii) PaPaRa: PaPaRa is a novel phylogeny-aware alignment procedure online
available from http://www.exelixis-lab.org/software.html. It can be applied
for alignment of small genomic reads with the reference phylogeny (Berger
and Stamatakis 2011).
(xiii) PhyloPythia: This is a phylogenetic tool that provides precise and useful
information about the generic clades of unidentified soil microorganisms
(Patil et al. 2012).
(xiv) Phymm: Phymm is another improved taxonomic classifier that categorises
very small metagenomic reads on the basis of the evolutionary background
(Brady and Salzberg 2011).
(xv) RAIphy: RAIphy is a good binning and phylogenetic tool that is used commonly for processing and categorization of the metagenomic reads along
with its efficient functional characterization (Albantoglu et al. 2011).
(xvi) SOrt-ITEMS: SOrt-ITEMS is a binning algorithm that employs alignment
parameters rather than the bit-score to find the phylogenetic relationships. It
can be downloaded from http://metagenomics.atc.tcs.com/binning/SOrtITEMS as mentioned by Monzoorul Haque et al. (2009)
(xvii) SPHINX: SPHINX is a mixed binning methodology that has good binning
potential through employing both ‘composition’- and ‘alignment’-based
binning algorithms. SPHINX is capable of analyzing metagenomic
sequences as quickly as composition-based algorithms and as efficiently as
alignment-based algorithms. It is online available from http://metagenomics.atc.tcs.com/SPHINX/ (Mohammed et al. 2011).
(xviii) TACOA: TACOA is a precise composite phylogenetic tool for ecological
metagenomic datasets with the potential to identify the taxonomy of large as
well as small reads (800 bp). It is transparent, rapid, and precise, and the
reference set can be simply updated with the availability of new genome
sequences (Diaz et al. 2009).
(xix) Treephyler: Treephyler allow users to establish a taxonomic relationship
among complex metagenomic datasets. Available from http://www.gobics.
de/fabian/treephyler.php (Schreiber et al. 2010).
6.2 Tools for Taxonomic Profiling
(ix) MetaPhyler: MetaPhyler is tool for predicting the phylogenetic relationship
and employs phylogenetic marker genes as a taxonomic reference.
Accessible from http://metaphyler.cbcb.umd.edu (Liu et al. 2011).
(x) MTR: MTR performs clustering through multiple taxonomic ranks instead
of lowest common ancestor (LCA). Rather than LCA, this precedes the
reads one at a time; MTR take advantage of information shared by reads. It
can be reached on http://cs.ru.nl/gori/software/MTR.tar.gz (Gori et al.
2011).
(xi) NBC: NBC is an online database employing the naïve Bayes classification
system for classification of entire metagenomic reads to their best taxonomic match. Publicly available at http://nbc.ece.drexel.edu (Rosen et al.
2011).
(xii) PaPaRa: PaPaRa is a novel phylogeny-aware alignment procedure online
available from http://www.exelixis-lab.org/software.html. It can be applied
for alignment of small genomic reads with the reference phylogeny (Berger
and Stamatakis 2011).
(xiii) PhyloPythia: This is a phylogenetic tool that provides precise and useful
information about the generic clades of unidentified soil microorganisms
(Patil et al. 2012).
(xiv) Phymm: Phymm is another improved taxonomic classifier that categorises
very small metagenomic reads on the basis of the evolutionary background
(Brady and Salzberg 2011).
(xv) RAIphy: RAIphy is a good binning and phylogenetic tool that is used commonly for processing and categorization of the metagenomic reads along
with its efficient functional characterization (Albantoglu et al. 2011).
(xvi) SOrt-ITEMS: SOrt-ITEMS is a binning algorithm that employs alignment
parameters rather than the bit-score to find the phylogenetic relationships. It
can be downloaded from http://metagenomics.atc.tcs.com/binning/SOrtITEMS as mentioned by Monzoorul Haque et al. (2009)
(xvii) SPHINX: SPHINX is a mixed binning methodology that has good binning
potential through employing both ‘composition’- and ‘alignment’-based
binning algorithms. SPHINX is capable of analyzing metagenomic
sequences as quickly as composition-based algorithms and as efficiently as
alignment-based algorithms. It is online available from http://metagenomics.atc.tcs.com/SPHINX/ (Mohammed et al. 2011).
(xviii) TACOA: TACOA is a precise composite phylogenetic tool for ecological
metagenomic datasets with the potential to identify the taxonomy of large as
well as small reads (800 bp). It is transparent, rapid, and precise, and the
reference set can be simply updated with the availability of new genome
sequences (Diaz et al. 2009).
(xix) Treephyler: Treephyler allow users to establish a taxonomic relationship
among complex metagenomic datasets. Available from http://www.gobics.
de/fabian/treephyler.php (Schreiber et al. 2010).
6.2 Tools for Taxonomic Profiling