Method name | Class of method | Sequence alignment method/Composition method | Standalonea/Web server | Most recent year published (first time published)b | Functional classification if applicable | References | Number of citationsc |
---|---|---|---|---|---|---|---|
MEGAN4 | Similarity | MEGABLAST, BLASTN, BLASTX, RAPSEARCH2 [32]Â / N/A | Yes/No | 2011 (2007) | KEGG, SEED | 1089 | |
MG-RAST | Similarity | BLASTN, BLATÂ / N/A | No/Yes | 2008 | SEED, NOG, COG, KEGG | [48] | 691 |
CAMERA | Similarity | All 6 BLAST programs / N/A | No/Yes | 2007 (2011) | Pfam, TIGRFAM, COG, KOG, PRK | 324 | |
CARMA3 | Similarity | BLASTX, HMMER3 [51]Â / N/A | Yes/Yes | 2011 (2008) | GO | 201 | |
WebMGA | Similarity | FR-HIT [54]Â / N/A | No/Yes | 2013 | Pfam, TIGRFAM, COG, KOG, PRK, GO | [55] | 54 |
DiScRIBinATE (SOrt-ITEMS)d | Similarity | BLASTX, RAPSEARCH2Â / N/A | Yes/No | 2010 (2009) | N/A | 48 | |
Ray Meta | Similarity | Exact match k-mers / N/A | Yes/No | 2012 | N/A | [57] | 34 |
Kraken | Similarity | Exact match k-mers / N/A | Yes/No | 2014 | N/A | [28] | 15 |
RTM | Similarity | k-mers / N/A | Yes/Yes | 2012 | KEGG | [58] | 12 |
Genometa | Similarity | Yes/No | 2012 | N/A | [61] | 7 | |
LMAT | Similarity | Exact match k-mers / N/A | Yes/No | 2013 | N/A | [62] | 6 |
Sequedex | Similarity | Exact match k-mers / N/A | Yes/No | 2012 | N/A | [63] | 5 |
MetaBin | Similarity | BLASTX, BLATÂ / N/A | Yes/Yes | 2012 | COG | [64] | 4 |
TAMER | Similarity | MEGABLASTÂ / N/A | Yes/No | 2012 | N/A | [65] | 4 |
metaBEETL | Similarity | Direct comparison of compressed text indices / N/A | Yes/No | 2013 | N/A | [7] | 2 |
SPANNER | Similarity | BLASTPÂ / N/A | Yes/No | 2013 | N/A | [66] | 2 |
GOTTCHA | Similarity | BWAÂ / N/A | Yes/No | 2015 | N/A | [67] | 0 |
CLARK | Similarity | k-mers / N/A | Yes/No | 2015 | N/A | [68] | 0 |
MLTreeMap | Marker | BLASTXÂ / N/A | Yes/Yes | 2010 (2007) | 4 Enzyme families | 206 | |
AMPHORA2 | Marker | HMMER3Â / N/A | Yes/Yes | 2012 (2008) | N/A | 190 | |
MetaPhlAn | Marker | MEGABLAST, Bowtie2 [73]Â / N/A | Yes/Yes | 2012 | N/A | [11] | 114 |
MetaPhyler | Marker | BLASTN, BLASTXÂ / N/A | Yes/No | 2011 | N/A | [30] | 42 |
mOTU | Marker | HMMER3Â / N/A | Yes/Yes | 2013 | N/A | [19] | 24 |
Phylosift | Marker | LAST, HMMER3Â / N/A | Yes/No | 2014 | N/A | [14] | 18 |
phymmBL | Hybrid | MEGABLASTÂ / IMM | Yes/No | 2011 (2009) | N/A | 182 | |
RITA | Hybrid | Pipeline of BLAST variations / NB | Yes/Yes | 2012 (2011) | N/A | 38 | |
SPHINX | Hybrid | BLASTXÂ / k-means | No/Yes | 2010 | N/A | [10] | 17 |
TaxyPro | Hybrid | CoMet web server / Mixture model | Yes/No | 2013 | Pfam | [77] | 3 |
TWARIT | Hybrid | BWA short read alignment [60]Â / k-means | No/Yes | 2012 | N/A | [78] | 2 |
PhyloPythiaS | Composition | N/AÂ / SVM | Yes/Yes | 2011 (2007) | N/A | 269 | |
TACOA | Composition | N/AÂ / k-NN | Yes/No | 2009 | N/A | [33] | 65 |
NBC | Composition | N/AÂ / NB | Yes/Yes | 2011 (2008) | N/A | 35 | |
RAIphy | Composition | N/AÂ / RAI | Yes/No | 2011 | N/A | [83] | 18 |
ClaMS | Composition | N/AÂ / DBC signature | Yes/No | 2011 | N/A | [84] | 10 |
INDUS | Composition | N/AÂ / k-means | No/Yes | 2011 | N/A | [85] | 8 |
TAC-ELM | Composition | N/AÂ / Neural Network | Yes/No | 2012 | N/A | [86] | 5 |
MetaCV | Composition | N/AÂ / CV | Yes/No | 2013 | KEGG | [87] | 4 |
GSTaxClassifier | Composition | N/AÂ / Bayesian | No/No | 2010 | N/A | [88] | 2 |