3 Reeder J, Knight R. Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods, 2010, 7: 668-669
[2]
4 Fonseca V G, Carvalho G R, Sung W, et al. Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nat Commun, 2010, 1: 98？？
[3]
6 Munch K, Boomsma W, Huelsenbeck J, et al. Statistical assignment of DNA sequences using Bayesian phylogenetics. Syst Biol, 2008, 57: 750-757？？
[4]
7 Caporaso J G, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods, 2010b, 7: 335-336
[5]
8 Hamilton H C, Strickland M S, Wickings K, et al. Surveying soil faunal communities using a direct molecular approach. Soil Biol Biochem, 2009, 41: 1311-1314？？
[6]
9 Wu T, Ayres E, Bardgett R D, et al. Molecular study of worldwide distribution and diversity of soil animals. Proc Natl Acad Sci USA, 2011, 108: 17720-17725？？
[7]
10 Bienert F, De Danieli S, Miquel C, et al. Tracking earthworm communities from soil DNA. Mol Ecol, 2012, 21: 2017-2030？？
[8]
5 Pruesse E, Quast C, Knittel K, et al. 2007 SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res, 2007, 35: 7188-7196？？
[9]
11 Epp L S, Boessenkool S, Bellemain E P, et al. New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Mol Ecol, 2012, 21: 1821-1833？？
[10]
12 Porazinska D L, Giblin-Davis R M, Esquivel A. Ecometagenetics confirms high tropical rainforest nematode diversity. Mol Ecol, 2010a, 19: 5521-5530
[11]
13 Porazinska D L, Giblin-Davis R M, Faller L, et al. Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity. Mol Ecol Resources, 2009, 9: 1439-1450？？
[12]
14 Porazinska D L, Sung W, Giblin-Davis R M, et al. Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure. Mol Ecol Resources, 2010b, 10: 666-676
[13]
15 Taberlet P, Coissac E, Hajibabaei M, et al. Environmental DNA. Mol Ecol, 2012, 21: 1789-1793？？
[14]
16 Yoccoz N G, Br？then K A, Gielly L, et al. DNA from soil mirrors plant taxonomic and growth form diversity. Mol Ecol, 2012, 21: 3647-3655？？
[15]
17 Koskinen J P, Holm L. SANS: high-throughput retrieval of protein sequences allowing 50% mismatches. Bioinformatics, 2012, 28: 438-443？？
[16]
18 Bik H M, Porazinska D L, Creer S, et al. Sequencing our way towardsunderstanding global eukaryoticbiodiversity. Cell, 2012, 27: 4
[17]
19 Smith B C, McAndrew T, Chen Z, et al. The cervical microbiome over 7 years and a comparison of methodologies for its characterization. PloS one, 2012, 7: 7
[18]
20 Lenz T, Becker S. Simple approach to reduce PCR artefact formation leads to reliable genotyping of MHC and other highly polymorphic loci—implications for evolutionary analysis. Gene, 2008, 427: 117-123？？
[19]
21 Coissac E, Riaz T, Puillandre N. Bioinformatic challenges for DNA metabarcoding of plants and animals. Mol Ecol, 2012, 21: 1834-1847？？
[20]
22 Taberlet P, Prud’Homme S M, Campione E, et al. Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies. Mol Ecol, 2012, 21: 1816-1820？？
[21]
23 Yoccoz N G, Br？then K A, Gielly L, et al. DNA from soil mirrors plant taxonomic and growth form diversity. Mol Ecol, 2012, 21: 3647-3655？？
[22]
24 Creer S, Fonseca V G, Porazinska D L, et al. Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Mol Ecol, 2010, 19: 4-20？？
[23]
25 Somerfield P J, Warwick R M, Moens T. Meiofauna techniques. In: Methods for the Study of Marine Benthos. Oxford: Blackwell Science Ltd., 2005. 229-272
[24]
26 Folmer O, Black M, Hoeh W, et al. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Marine Biol Biotechnol, 1994, 3: 294-299
[25]
27 Edgar R C, Haas B J, Clemente J C, et al. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 2011, 27: 2194-2200？？
[26]
28 Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 2006, 22: 1658-1659？？
[27]
29 Yu D W, Ji Y Q, Emerson B C, et al. Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods Ecol Evol, 2012, 3: 613-623？？
[28]
30 Haas B J, Gevers D, Earl A M, et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res, 2011, 21: 494-504？？
[29]
31 Chou H H, Holmes M H. DNA sequence quality trimming and vector removal. Bioinformatics, 2001, 17: 1093-1104？？
[30]
32 Edgar R C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res, 2004, 32: 1792-1797？？
[31]
33 Amend A S, Seifert K A, Bruns T D. Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Mol Ecol, 2010, 19: 5555-5565
[32]
34 Gotelli N J, Colwell R K. Estimating species richness. In: Meagurran A E, McGill B J, eds. Biological Diversity: Frontiers in Measurement and Assessment. Oxford: Oxford University Press, 2011. 39-54
[33]
35 Nipperess D. Phylocurve: an R function for generating a rarefaction curve of phylogenetic diversity. http://davidnipperess.blogspot.com/ 2012/07/phylocurve-r-function-for-generating.html, 2011
[34]
36 R Development Core Team. R: a language and environment for statistical computing. In: R Foundation for Statistical Computing, Vienna, Austria, 2012
[35]
37 Kearse M, Moir R, Wioson A, et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinf Appl Note, 2012, 28: 1647-1649
[36]
38 Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol, 2003, 52: 696-704？？
[37]
39 Yang X D, Sha L Q. Species composition and diversity of soil mesofauna in the ‘Holy Hills’ fragmentary tropical rain forest of Xishuangbanna, China. Chin J Appl Ecol, 2010, 12: 261-265
[38]
41 Faith D P, Baker A M. Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges. Evol Bioinf Online, 2006, 2: 121-128
[39]
42 Matsen F A, Kodner R B, Armbrust E V. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics, 2010, 11: 538？？
[40]
40 Caporaso J G, Bittinger K, Bushman F D, et al. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics, 2010a, 26: 266-267
[41]
1 Edgar R C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 2010, 26: 2460-2461？？
[42]
2 Hao X, Jiang R, Chen T. Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. Bioinformatics, 2011, 27: 611-618？？
