A comparative evaluation of sequence classification programs

Bazinet, Adam L; Cummings, Michael P

doi:10.1186/1471-2105-13-92

BMC Bioinformatics

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

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com