66
(xiii) Greengenes: Green genes are a 16S rRNA gene database frequently utilized
for identifying chimeras, providing a platform for alignment and evolutionary
linkage. It is online accessible from http://greengenes.lbl.gov as reported earlier (DeSantis et al. 2006).
(xiv) RDP database: The Ribosomal-Database-Project facilitates researchers for
quality-control analysis of bacteria and archaea on the basis of highly conserved gene sequences. RDP is online available from http://rdp.cme.msu.edu/
and explained well (Cole et al. 2009).
6.2 Tools for Taxonomic Profiling
(i) Amphora2: AMPHORA2 is an automated phylogenetic inference approach
that can be directly applied for high-throughput and high-quality genome
tree building and metagenomic phylotyping. AMPHORA2 is available at
http://wolbachia.biology.virginia.edu/WuLab/Software.html (Wu and Scott
2012)
(ii) CARMA3: CARMA3 is a tool for community structure identification from
processed and unprocessed metagenomic reads and is compatible with many
homologies searches. It is online available on following web-link http://
webcarma.cebitec.uni-bielefeld.de (Gerlach and Stoye 2011).
(iii) ClaMS: Classifier for Metagenomic Sequences, abbreviated as ClaMS is a
Java-enabled desktop application for binning of assembled contigs in
metagenomic datasets through user-specified training sets and initial parameters (Pati et al. 2011).
(iv) DiScRIBinATE: DiScRIBinATE (Distance-Score Ratio for Improved
Binning And Taxonomic Estimation) is a fast and accurate binning method
for navigating the evolutionary relationship within the huge metagenome
(Ghosh et al. 2010).
(v) INDUS: INDUS is a fast binning tool, capable of quickly categorizing massive reads under modelled and real data with better efficacy than composition approaches. The INDUS tool can be accessed at http://metagenomics.
atc.tcs.com/INDUS/ (Mohammed et al. 2011).
(vi) MARTA: MARTA provides a Java platform for studying the evolutionary
relationship among the gene sequences and depends on NCBI tools such as
BLAST software and the Taxonomy database (Horton et al. 2010).
(vii) MetaCluster: MetaCluster is an unsupervised binning tool that can be utilized for the effective and precise grouping of small reads among myriads of
species (Wang et al. 2012).
(viii) MetaPhlAn: MetaPhlAn is a metagenomic phylogenetic analysis tool that
utilizes clade-specific marker genes for definite assignment of reads to
microbial clades in a fast and accurate manner. It is online available from
http://huttenhower.sph.harvard.edu/metaphlan/ (Segata et al. 2012).
6 Bioinformatics Tools for Soil Microbiome Analysis
(xiii) Greengenes: Green genes are a 16S rRNA gene database frequently utilized
for identifying chimeras, providing a platform for alignment and evolutionary
linkage. It is online accessible from http://greengenes.lbl.gov as reported earlier (DeSantis et al. 2006).
(xiv) RDP database: The Ribosomal-Database-Project facilitates researchers for
quality-control analysis of bacteria and archaea on the basis of highly conserved gene sequences. RDP is online available from http://rdp.cme.msu.edu/
and explained well (Cole et al. 2009).
6.2 Tools for Taxonomic Profiling
(i) Amphora2: AMPHORA2 is an automated phylogenetic inference approach
that can be directly applied for high-throughput and high-quality genome
tree building and metagenomic phylotyping. AMPHORA2 is available at
http://wolbachia.biology.virginia.edu/WuLab/Software.html (Wu and Scott
2012)
(ii) CARMA3: CARMA3 is a tool for community structure identification from
processed and unprocessed metagenomic reads and is compatible with many
homologies searches. It is online available on following web-link http://
webcarma.cebitec.uni-bielefeld.de (Gerlach and Stoye 2011).
(iii) ClaMS: Classifier for Metagenomic Sequences, abbreviated as ClaMS is a
Java-enabled desktop application for binning of assembled contigs in
metagenomic datasets through user-specified training sets and initial parameters (Pati et al. 2011).
(iv) DiScRIBinATE: DiScRIBinATE (Distance-Score Ratio for Improved
Binning And Taxonomic Estimation) is a fast and accurate binning method
for navigating the evolutionary relationship within the huge metagenome
(Ghosh et al. 2010).
(v) INDUS: INDUS is a fast binning tool, capable of quickly categorizing massive reads under modelled and real data with better efficacy than composition approaches. The INDUS tool can be accessed at http://metagenomics.
atc.tcs.com/INDUS/ (Mohammed et al. 2011).
(vi) MARTA: MARTA provides a Java platform for studying the evolutionary
relationship among the gene sequences and depends on NCBI tools such as
BLAST software and the Taxonomy database (Horton et al. 2010).
(vii) MetaCluster: MetaCluster is an unsupervised binning tool that can be utilized for the effective and precise grouping of small reads among myriads of
species (Wang et al. 2012).
(viii) MetaPhlAn: MetaPhlAn is a metagenomic phylogenetic analysis tool that
utilizes clade-specific marker genes for definite assignment of reads to
microbial clades in a fast and accurate manner. It is online available from
http://huttenhower.sph.harvard.edu/metaphlan/ (Segata et al. 2012).
6 Bioinformatics Tools for Soil Microbiome Analysis