Table 1

Program attributes and characteristics
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

Bazinet and Cummings

Bazinet and Cummings BMC Bioinformatics 2012 13:92   doi:10.1186/1471-2105-13-92

Open Data