-
1
-
-
84881138595
-
Insights into the phylogeny and coding potential of microbial dark matter
-
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 2013;499(7459):431-7.
-
(2013)
Nature
, vol.499
, Issue.7459
, pp. 431-437
-
-
Rinke, C.1
Schwientek, P.2
Sczyrba, A.3
Ivanova, N.N.4
Anderson, I.J.5
Cheng, J.F.6
Darling, A.7
Malfatti, S.8
Swan, B.K.9
Gies, E.A.10
-
2
-
-
84966929319
-
A new view of the tree of life
-
Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, et al. A new view of the tree of life. Nat Microbiol. 2016;1(5):16048.
-
(2016)
Nat Microbiol
, vol.1
, Issue.5
, pp. 16048
-
-
Hug, L.A.1
Baker, B.J.2
Anantharaman, K.3
Brown, C.T.4
Probst, A.J.5
Castelle, C.J.6
Butterfield, C.N.7
Hernsdorf, A.W.8
Amano, Y.9
Ise, K.10
-
3
-
-
84957922843
-
Single-cell-genomics-facilitated read binning of candidate phylum EM19 genomes from geothermal spring metagenomes
-
Becraft ED, Dodsworth JA, Murugapiran SK, Ohlsson JI, Briggs BR, Kanbar J, De Vlaminck I, Quake SR, Dong HL, Hedlund BP, et al. Single-cell-genomics-facilitated read binning of candidate phylum EM19 genomes from geothermal spring metagenomes. Appl Environ Microb. 2016;82(4):992-1003.
-
(2016)
Appl Environ Microb
, vol.82
, Issue.4
, pp. 992-1003
-
-
Becraft, E.D.1
Dodsworth, J.A.2
Murugapiran, S.K.3
Ohlsson, J.I.4
Briggs, B.R.5
Kanbar, J.6
De Vlaminck, I.7
Quake, S.R.8
Dong, H.L.9
Hedlund, B.P.10
-
4
-
-
84961121702
-
Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C-1 Compound Oxidation
-
Denef VJ, Mueller RS, Chiang EN, Liebig JR, Vanderploeg HA. Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C-1 Compound Oxidation. Appl Environ Microb. 2016;82(5):1423-32.
-
(2016)
Appl Environ Microb
, vol.82
, Issue.5
, pp. 1423-1432
-
-
Denef, V.J.1
Mueller, R.S.2
Chiang, E.N.3
Liebig, J.R.4
Vanderploeg, H.A.5
-
5
-
-
84944739223
-
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics
-
Evans PN, Parks DH, Chadwick GL, Robbins SJ, Orphan VJ, Golding SD, Tyson GW. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science. 2015;350(6259):434-8.
-
(2015)
Science
, vol.350
, Issue.6259
, pp. 434-438
-
-
Evans, P.N.1
Parks, D.H.2
Chadwick, G.L.3
Robbins, S.J.4
Orphan, V.J.5
Golding, S.D.6
Tyson, G.W.7
-
6
-
-
84940446833
-
Auxotrophy and intrapopulation complementary in the "interactome" of a cultivated freshwater model community
-
Garcia SL, Buck M, McMahon KD, Grossart HP, Eiler A, Warnecke F. Auxotrophy and intrapopulation complementary in the "interactome" of a cultivated freshwater model community. Mol Ecol. 2015;24(17):4449-59.
-
(2015)
Mol Ecol
, vol.24
, Issue.17
, pp. 4449-4459
-
-
Garcia, S.L.1
Buck, M.2
McMahon, K.D.3
Grossart, H.P.4
Eiler, A.5
Warnecke, F.6
-
7
-
-
84940704651
-
Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage
-
Hiras J, YW W, Eichorst SA, Simmons BA, Singer SW. Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage. Isme J. 2016;10(4):833-45.
-
(2016)
Isme J
, vol.10
, Issue.4
, pp. 833-845
-
-
Hiras, J.1
Y.W, W.2
Eichorst, S.A.3
Simmons, B.A.4
Singer, S.W.5
-
8
-
-
84929340364
-
Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes
-
Hultman J, Waldrop MP, Mackelprang R, David MM, McFarland J, Blazewicz SJ, Harden J, Turetsky MR, McGuire AD, Shah MB, et al. Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature. 2015;521(7551):208-12.
-
(2015)
Nature
, vol.521
, Issue.7551
, pp. 208-212
-
-
Hultman, J.1
Waldrop, M.P.2
Mackelprang, R.3
David, M.M.4
McFarland, J.5
Blazewicz, S.J.6
Harden, J.7
Turetsky, M.R.8
McGuire, A.D.9
Shah, M.B.10
-
9
-
-
84953884747
-
Identification and resolution of microdiversity through metagenomic sequencing of parallel consortia
-
Nelson WC, Maezato Y, YW W, Romine MF, Lindemann SR. Identification and resolution of microdiversity through metagenomic sequencing of parallel consortia. Appl Environ Microb. 2016;82(1):255-67.
-
(2016)
Appl Environ Microb
, vol.82
, Issue.1
, pp. 255-267
-
-
Nelson, W.C.1
Maezato, Y.2
Y.W, W.3
Romine, M.F.4
Lindemann, S.R.5
-
10
-
-
84959529863
-
Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methylreducing methanogen
-
Nobu MK, Narihiro T, Kuroda K, Mei R, Liu WT. Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methylreducing methanogen. Isme J. 2016;10(10):2478-87.
-
(2016)
Isme J
, vol.10
, Issue.10
, pp. 2478-2487
-
-
Nobu, M.K.1
Narihiro, T.2
Kuroda, K.3
Mei, R.4
Liu, W.T.5
-
11
-
-
85021200372
-
Metagenomic evidence for the presence of Comammox Nitrospira-like bacteria in a drinking water system
-
Pinto AJ, Marcus DN, Ijaz UZ, Santos QMBD, Dick GJ, Raskin L. Metagenomic evidence for the presence of Comammox Nitrospira-like bacteria in a drinking water system. Msphere. 2016;1(1):e00054-15.
-
(2016)
Msphere
, vol.1
, Issue.1
, pp. e00015-e00054
-
-
Pinto, A.J.1
Marcus, D.N.2
Ijaz, U.Z.3
Santos, Q.M.B.D.4
Dick, G.J.5
Raskin, L.6
-
12
-
-
84962090377
-
Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda Lake brines
-
Vavourakis CD, Ghai R, Rodriguez-Valera F, Sorokin DY, Tringe SG, Hugenholtz P, Muyzer G. Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda Lake brines. Front Microbiol. 2016;7:211.
-
(2016)
Front Microbiol
, vol.7
, pp. 211
-
-
Vavourakis, C.D.1
Ghai, R.2
Rodriguez-Valera, F.3
Sorokin, D.Y.4
Tringe, S.G.5
Hugenholtz, P.6
Muyzer, G.7
-
13
-
-
84879678051
-
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
-
Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol. 2013;31(6):533-8.
-
(2013)
Nat Biotechnol
, vol.31
, Issue.6
, pp. 533-538
-
-
Albertsen, M.1
Hugenholtz, P.2
Skarshewski, A.3
Nielsen, K.L.4
Tyson, G.W.5
Nielsen, P.H.6
-
14
-
-
84908597294
-
Binning metagenomic contigs by coverage and composition
-
Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C. Binning metagenomic contigs by coverage and composition. Nat Methods. 2014;11:1144-6.
-
(2014)
Nat Methods
, vol.11
, pp. 1144-1146
-
-
Alneberg, J.1
Bjarnason, B.S.2
de Bruijn, I.3
Schirmer, M.4
Quick, J.5
Ijaz, U.Z.6
Lahti, L.7
Loman, N.J.8
Andersson, A.F.9
Quince, C.10
-
15
-
-
84907682734
-
GroopM: an automated tool for the recovery of population genomes from related metagenomes
-
Imelfort M, Parks D, Woodcroft BJ, Dennis P, Hugenholtz P, Tyson GW. GroopM: an automated tool for the recovery of population genomes from related metagenomes. Peerj. 2014;2:e603.
-
(2014)
Peerj
, vol.2
-
-
Imelfort, M.1
Parks, D.2
Woodcroft, B.J.3
Dennis, P.4
Hugenholtz, P.5
Tyson, G.W.6
-
16
-
-
84940387197
-
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
-
Kang DWD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. Peerj. 2015;3:e1165.
-
(2015)
Peerj
, vol.3
-
-
Kang, D.W.D.1
Froula, J.2
Egan, R.3
Wang, Z.4
-
17
-
-
84938483160
-
VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data
-
Laczny CC, Sternal T, Plugaru V, Gawron P, Atashpendar A, Margossian HH, Coronado S, van der Maaten L, Vlassis N, Wilmes P. VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data. Microbiome. 2015;3:1.
-
(2015)
Microbiome
, vol.3
, pp. 1
-
-
Laczny, C.C.1
Sternal, T.2
Plugaru, V.3
Gawron, P.4
Atashpendar, A.5
Margossian, H.H.6
Coronado, S.7
van der Maaten, L.8
Vlassis, N.9
Wilmes, P.10
-
18
-
-
84963800052
-
Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes
-
Lin HH, Liao YC. Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes. Sci Rep-Uk. 2016;6:24175.
-
(2016)
Sci Rep-Uk
, vol.6
, pp. 24175
-
-
Lin, H.H.1
Liao, Y.C.2
-
19
-
-
85018348728
-
COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge
-
YY L, Chen T, Fuhrman JA, Sun FZ. COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge. Bioinformatics. 2017;33(6):791-8.
-
(2017)
Bioinformatics
, vol.33
, Issue.6
, pp. 791-798
-
-
Y.Y, L.1
Chen, T.2
Fuhrman, J.A.3
Sun, F.Z.4
-
20
-
-
84875832926
-
The binning of metagenomic contigs for microbial physiology of mixed cultures
-
Strous M, Kraft B, Bisdorf R, Tegetmeyer HE. The binning of metagenomic contigs for microbial physiology of mixed cultures. Front Microbiol. 2012;3:410.
-
(2012)
Front Microbiol
, vol.3
, pp. 410
-
-
Strous, M.1
Kraft, B.2
Bisdorf, R.3
Tegetmeyer, H.E.4
-
21
-
-
84957911451
-
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
-
YW W, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016;32(4):605-7.
-
(2016)
Bioinformatics
, vol.32
, Issue.4
, pp. 605-607
-
-
Y.W, W.1
Simmons, B.A.2
Singer, S.W.3
-
22
-
-
84925636192
-
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
-
YW W, Tang YH, Tringe SG, Simmons BA, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014;2:26.
-
(2014)
Microbiome
, vol.2
, pp. 26
-
-
Y.W, W.1
Tang, Y.H.2
Tringe, S.G.3
Simmons, B.A.4
Singer, S.W.5
-
23
-
-
0035174578
-
The species concept for prokaryotes
-
Rossello-Mora R, Amann R. The species concept for prokaryotes. FEMS Microbiol Rev. 2001;25(1):39-67.
-
(2001)
FEMS Microbiol Rev
, vol.25
, Issue.1
, pp. 39-67
-
-
Rossello-Mora, R.1
Amann, R.2
-
24
-
-
0035989633
-
Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology
-
Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kampfer P, Maiden MCJ, Nesme X, Rossello-Mora R, Swings J, Truper HG, et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Micr. 2002;52:1043-7.
-
(2002)
Int J Syst Evol Micr
, vol.52
, pp. 1043-1047
-
-
Stackebrandt, E.1
Frederiksen, W.2
Garrity, G.M.3
Grimont, P.A.D.4
Kampfer, P.5
Maiden, M.C.J.6
Nesme, X.7
Rossello-Mora, R.8
Swings, J.9
Truper, H.G.10
-
25
-
-
79959422558
-
Meta-IDBA: a de Novo assembler for metagenomic data
-
Peng Y, Leung HCM, Yiu SM, Chin FYL. Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics. 2011;27(13):I94-I101.
-
(2011)
Bioinformatics
, vol.27
, Issue.13
, pp. I94-I101
-
-
Peng, Y.1
Leung, H.C.M.2
Yiu, S.M.3
Chin, F.Y.L.4
-
26
-
-
84860771820
-
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
-
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455-77.
-
(2012)
J Comput Biol
, vol.19
, Issue.5
, pp. 455-477
-
-
Bankevich, A.1
Nurk, S.2
Antipov, D.3
Gurevich, A.A.4
Dvorkin, M.5
Kulikov, A.S.6
Lesin, V.M.7
Nikolenko, S.I.8
Pham, S.9
Prjibelski, A.D.10
-
27
-
-
84871396799
-
Ray meta: scalable de novo metagenome assembly and profiling
-
Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J. Ray meta: scalable de novo metagenome assembly and profiling. Genome Biol. 2012;13(12):R122.
-
(2012)
Genome Biol
, vol.13
, Issue.12
, pp. R122
-
-
Boisvert, S.1
Raymond, F.2
Godzaridis, E.3
Laviolette, F.4
Corbeil, J.5
-
28
-
-
84929626808
-
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
-
Li DH, Liu CM, Luo RB, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31(10):1674-6.
-
(2015)
Bioinformatics
, vol.31
, Issue.10
, pp. 1674-1676
-
-
Li, D.H.1
Liu, C.M.2
Luo, R.B.3
Sadakane, K.4
Lam, T.W.5
-
29
-
-
79956041561
-
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
-
Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF. EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol. 2011;12(5):R44.
-
(2011)
Genome Biol
, vol.12
, Issue.5
, pp. R44
-
-
Miller, C.S.1
Baker, B.J.2
Thomas, B.C.3
Singer, S.W.4
Banfield, J.F.5
-
30
-
-
84893511241
-
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
-
Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Micr. 2014;64:346-51.
-
(2014)
Int J Syst Evol Micr
, vol.64
, pp. 346-351
-
-
Kim, M.1
Oh, H.S.2
Park, S.C.3
Chun, J.4
-
31
-
-
84874011652
-
Genome sequence-based species delimitation with confidence intervals and improved distance functions
-
Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. Bmc Bioinformatics. 2013;14:60.
-
(2013)
Bmc Bioinformatics
, vol.14
, pp. 60
-
-
Meier-Kolthoff, J.P.1
Auch, A.F.2
Klenk, H.P.3
Goker, M.4
-
32
-
-
73149098333
-
Shifting the genomic gold standard for the prokaryotic species definition
-
Richter M, Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. PNAS. 2009;106(45):19126-31.
-
(2009)
PNAS
, vol.106
, Issue.45
, pp. 19126-19131
-
-
Richter, M.1
Rossello-Mora, R.2
-
33
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of bacteria and archaea
-
DY W, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature. 2009;462(7276):1056-60.
-
(2009)
Nature
, vol.462
, Issue.7276
, pp. 1056-1060
-
-
D.Y, W.1
Hugenholtz, P.2
Mavromatis, K.3
Pukall, R.4
Dalin, E.5
Ivanova, N.N.6
Kunin, V.7
Goodwin, L.8
Wu, M.9
Tindall, B.J.10
-
34
-
-
0034942865
-
Universal trees based on large combined protein sequence data sets
-
Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ. Universal trees based on large combined protein sequence data sets. Nat Genet. 2001;28(3):281-5.
-
(2001)
Nat Genet
, vol.28
, Issue.3
, pp. 281-285
-
-
Brown, J.R.1
Douady, C.J.2
Italia, M.J.3
Marshall, W.E.4
Stanhope, M.J.5
-
35
-
-
84885819796
-
Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups
-
DY W, Jospin G, Eisen JA. Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLoS One. 2013;8(10):e77033.
-
(2013)
PLoS One
, vol.8
, Issue.10
-
-
D.Y, W.1
Jospin, G.2
Eisen, J.A.3
-
36
-
-
33644700003
-
Toward automatic reconstruction of a highly resolved tree of life
-
Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science. 2006;311(5765):1283-7.
-
(2006)
Science
, vol.311
, Issue.5765
, pp. 1283-1287
-
-
Ciccarelli, F.D.1
Doerks, T.2
von Mering, C.3
Creevey, C.J.4
Snel, B.5
Bork, P.6
-
37
-
-
84861342496
-
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage
-
Dupont CL, Rusch DB, Yooseph S, Lombardo MJ, Richter RA, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH, et al. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. Isme J. 2012;6(6):1186-99.
-
(2012)
Isme J
, vol.6
, Issue.6
, pp. 1186-1199
-
-
Dupont, C.L.1
Rusch, D.B.2
Yooseph, S.3
Lombardo, M.J.4
Richter, R.A.5
Valas, R.6
Novotny, M.7
Yee-Greenbaum, J.8
Selengut, J.D.9
Haft, D.H.10
-
38
-
-
33847280283
-
Prediction of effective genome size in metagenomic samples.
-
Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P. Prediction of effective genome size in metagenomic samples. Genome Biol. 2007;8(1)
-
(2007)
Genome Biol.
, vol.8
, Issue.1
-
-
Raes, J.1
Korbel, J.O.2
Lercher, M.J.3
von Mering, C.4
Bork, P.5
-
39
-
-
84937040910
-
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
-
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25(7):1043-55.
-
(2015)
Genome Res
, vol.25
, Issue.7
, pp. 1043-1055
-
-
Parks, D.H.1
Imelfort, M.2
Skennerton, C.T.3
Hugenholtz, P.4
Tyson, G.W.5
-
40
-
-
77952299957
-
Prodigal: prokaryotic gene recognition and translation initiation site identification
-
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. Bmc Bioinformatics. 2010;11:119.
-
(2010)
Bmc Bioinformatics
, vol.11
, pp. 119
-
-
Hyatt, D.1
Chen, G.L.2
Locascio, P.F.3
Land, M.L.4
Larimer, F.W.5
Hauser, L.J.6
-
41
-
-
78651326786
-
FragGeneScan: predicting genes in short and error-prone reads
-
Rho MN, Tang HX, Ye YZ. FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res. 2010;38(20):e191.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.20
-
-
Rho, M.N.1
Tang, H.X.2
Ye, Y.Z.3
-
42
-
-
84976865403
-
The Pfam protein families database: towards a more sustainable future
-
Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016;44(D1):D279-85.
-
(2016)
Nucleic Acids Res
, vol.44 D1
, pp. D279-D285
-
-
Finn, R.D.1
Coggill, P.2
Eberhardt, R.Y.3
Eddy, S.R.4
Mistry, J.5
Mitchell, A.L.6
Potter, S.C.7
Punta, M.8
Qureshi, M.9
Sangrador-Vegas, A.10
-
43
-
-
77952988108
-
A new generation of homology search tools based on probabilistic inference
-
Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform. 2009;23(1):205-11.
-
(2009)
Genome Inform
, vol.23
, Issue.1
, pp. 205-211
-
-
Eddy, S.R.1
-
44
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792-7.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.5
, pp. 1792-1797
-
-
Edgar, R.C.1
-
45
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
-
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000;17(4):540-52.
-
(2000)
Mol Biol Evol
, vol.17
, Issue.4
, pp. 540-552
-
-
Castresana, J.1
-
46
-
-
67649327176
-
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix
-
Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26(7):1641-50.
-
(2009)
Mol Biol Evol
, vol.26
, Issue.7
, pp. 1641-1650
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
47
-
-
85022158148
-
MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets
-
Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870-4.
-
(2016)
Mol Biol Evol
, vol.33
, Issue.7
, pp. 1870-1874
-
-
Kumar, S.1
Stecher, G.2
Tamura, K.3
-
48
-
-
0030203863
-
TreeView: an application to display phylogenetic trees on personal computers
-
Page RDM. TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci. 1996;12(4):357-8.
-
(1996)
Comput Appl Biosci
, vol.12
, Issue.4
, pp. 357-358
-
-
Page, R.D.M.1
-
49
-
-
85040763963
-
-
Last access date: May 10, 2017.
-
FigTree [ http://tree.bio.ed.ac.uk/software/figtree/ ] Last access date: May 10, 2017.
-
-
-
-
50
-
-
84899553363
-
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
-
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312-3.
-
(2014)
Bioinformatics
, vol.30
, Issue.9
, pp. 1312-1313
-
-
Stamatakis, A.1
-
51
-
-
0034849408
-
MRBAYES: Bayesian inference of phylogenetic trees
-
Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 2001;17(8):754-5.
-
(2001)
Bioinformatics
, vol.17
, Issue.8
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
52
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
-
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59(3):307-21.
-
(2010)
Syst Biol
, vol.59
, Issue.3
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
53
-
-
84922362345
-
IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies
-
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268-74.
-
(2015)
Mol Biol Evol
, vol.32
, Issue.1
, pp. 268-274
-
-
Nguyen, L.T.1
Schmidt, H.A.2
von Haeseler, A.3
Minh, B.Q.4
-
54
-
-
85040768125
-
-
Last access date: April 3
-
Gene oncology download mappings [ http://www.geneontology.org/page/download-mappings ] Last access date: April 3, 2017.
-
(2017)
-
-
-
55
-
-
85040764529
-
-
Last access date: March 13, 2017.
-
NCBI COGs [ https://www.ncbi.nlm.nih.gov/COG/index.html ] Last access date: March 13, 2017.
-
-
-
-
56
-
-
85015824737
-
Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads
-
Huson DH, Tappu R, Bazinet AL, Xie C, Cummings MP, Nieselt K, Williams R. Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads. Microbiome. 2017;5:11.
-
(2017)
Microbiome
, vol.5
, pp. 11
-
-
Huson, D.H.1
Tappu, R.2
Bazinet, A.L.3
Xie, C.4
Cummings, M.P.5
Nieselt, K.6
Williams, R.7
-
57
-
-
85027935288
-
Methanogenic paraffin degradation proceeds via alkane addition to fumarate by 'Smithella' spp. mediated by a syntrophic coupling with hydrogenotrophic methanogens
-
Wawrik B, Marks CR, Davidova IA, McInerney MJ, Pruitt S, Duncan KE, Suflita JM, Callaghan AV. Methanogenic paraffin degradation proceeds via alkane addition to fumarate by 'Smithella' spp. mediated by a syntrophic coupling with hydrogenotrophic methanogens. Environ Microbiol. 2016;18(8):2604-19.
-
(2016)
Environ Microbiol
, vol.18
, Issue.8
, pp. 2604-2619
-
-
Wawrik, B.1
Marks, C.R.2
Davidova, I.A.3
McInerney, M.J.4
Pruitt, S.5
Duncan, K.E.6
Suflita, J.M.7
Callaghan, A.V.8
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