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Table 1 Program attributes and characteristics

From: A comparative evaluation of sequence classification programs

Similarity-based Methods
Program Similarity Method LCA Specific Genes Req’d Interface
CARMA BLAST, HMM     command line, web-based
FACS other     command line
jMOTU/Taxonerator BLAST, other    multiple alignment command line
MARTA BLAST LCA-like   command line
MEGAN BLAST LCA-like   GUI
MetaPhyler BLAST    marker genes command line
MG-RAST BLAST    marker genes web-based
MTR BLAST LCA-like   command line
SOrt-ITEMS BLAST LCA-like   command line
Composition-based Methods   
Program Composition Method Machine Learning Confidence Method Specific Genes Req’d Interface
Naive Bayes Classifier NBC supervised other   command line, web-based
PhyloPythiaS other supervised    command line, web-based
PhymmBL IMM supervised other   command line
RAIphy other semi-supervised    GUI
RDP k-means/kNN, NBC supervised bootstrap 16S rRNA command line, web-based
Scimm IMM semi-supervised    command line
TACOA k-means/kNN supervised    command line
Phylogeny-based Methods   
Program Phylogeny Method Confidence Method Specific Genes Req’d Interface
EPA ML bootstrap, other multiple alignment command line, web-based
FastTree other bootstrap multiple alignment command line
green genes (NAST, Simrank) other    16S rRNA web-based
pplacer ML, Bayesian posterior probability, other multiple alignment command line
Combined Similarity and Composition-based Methods   
Program Similarity Method Composition Method Machine Learning Specific Genes Req’d Interface
SPHINX BLAST k-means/kNN supervised   web-based
Combined Similarity and Phylogeny-based Methods   
Program Similarity Method Phylogeny Method Confidence Method Specific Genes Req’d Interface
AMPHORA HMM other bootstrap marker genes command line
MLTreeMap BLAST, HMM ML bootstrap, other marker genes command line, web-based
SAP BLAST Bayesian, other posterior probability, other   command line
Treephyler HMM other bootstrap marker genes command line
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BMC Bioinformatics

ISSN: 1471-2105

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