SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles

Rapid identification of high-confidence taxonomic assignments for metagenomic data

(2012) Norman J. MacDonald et al.   NUCLEIC ACIDS RESEARCH

Classifying short genomic fragments from novel lineages using composition and homology

(2011) Donovan H Parks et al.   BMC BIOINFORMATICS

Taxonomic metagenome sequence assignment with structured output models

(2011) Kaustubh R Patil et al.   NATURE METHODS

Taxonomic classification of metagenomic shotgun sequences with CARMA3

(2011) Wolfgang Gerlach et al.   NUCLEIC ACIDS RESEARCH

Distinguishing Microbial Genome Fragments Based on Their Composition: Evolutionary and Comparative Genomic Perspectives

(2010) Scott C. Perry et al.   Genome Biology and Evolution

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

(2009) M. Monzoorul Haque et al.   BIOINFORMATICS

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

(2009) Naryttza N Diaz et al.   BMC BIOINFORMATICS

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS