-
1
-
-
42149157760
-
Broad phylogenomic sampling improves resolution of the animal tree of life
-
10.1038/nature06614, 18322464
-
Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sørensen MV, Haddock SHD, Schmidt-Rhaesa A, Okusu A, Kristensen RM, Wheeler WC, Martindale MQ, Giribet G. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 2008, 452(7188):745-749. [http://dx.doi.org/10.1038/nature06614], 10.1038/nature06614, 18322464.
-
(2008)
Nature
, vol.452
, Issue.7188
, pp. 745-749
-
-
Dunn, C.W.1
Hejnol, A.2
Matus, D.Q.3
Pang, K.4
Browne, W.E.5
Smith, S.A.6
Seaver, E.7
Rouse, G.W.8
Obst, M.9
Edgecombe, G.D.10
Sørensen, M.V.11
Haddock, S.H.D.12
Schmidt-Rhaesa, A.13
Okusu, A.14
Kristensen, R.M.15
Wheeler, W.C.16
Martindale, M.Q.17
Giribet, G.18
-
2
-
-
72749099971
-
Assessing the root of bilaterian animals with scalable phylogenomic methods
-
10.1098/rspb.2009.0896, 2817096, 19759036
-
Hejnol A, Obst M, Stamatakis A, Ott M, Rouse GW, Edgecombe GD, Martinez P, Baguñà J, Bailly X, Jondelius U, Wiens M, Müller WEG, Seaver E, Wheeler WC, Martindale MQ, Giribet G, Dunn CW. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc R Soc B 2009, 276(1677):4261-4270. 10.1098/rspb.2009.0896, 2817096, 19759036.
-
(2009)
Proc R Soc B
, vol.276
, Issue.1677
, pp. 4261-4270
-
-
Hejnol, A.1
Obst, M.2
Stamatakis, A.3
Ott, M.4
Rouse, G.W.5
Edgecombe, G.D.6
Martinez, P.7
Baguñà, J.8
Bailly, X.9
Jondelius, U.10
Wiens, M.11
Müller, W.E.G.12
Seaver, E.13
Wheeler, W.C.14
Martindale, M.Q.15
Giribet, G.16
Dunn, C.W.17
-
3
-
-
83555166100
-
Resolving the evolutionary relationships of molluscs with phylogenomic tools
-
10.1038/nature10526, 22031330
-
Smith SA, Wilson NG, Goetz FE, Feehery C, Andrade SCS, Rouse GW, Giribet G, Dunn CW. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature 2011, 480(7377):364-367. 10.1038/nature10526, 22031330.
-
(2011)
Nature
, vol.480
, Issue.7377
, pp. 364-367
-
-
Smith, S.A.1
Wilson, N.G.2
Goetz, F.E.3
Feehery, C.4
Andrade, S.C.S.5
Rouse, G.W.6
Giribet, G.7
Dunn, C.W.8
-
4
-
-
65249099546
-
Phylogenomics Revives Traditional Views on Deep Animal Relationships
-
Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, Boury-Esnault N, Vacelet J, Renard E, Houliston E, QuEinnec E, Da Silva C, Wincker P, Le Guyader H, Leys S, Jackson DJ, Schreiber F, Erpenbeck D, Morgenstern B, WOrheide G, Manuel M. Phylogenomics Revives Traditional Views on Deep Animal Relationships. Curr Biol : CB 2009, 19(8):706-712. [http://dx.doi.org/10.1016/j.cub.2009.02.052].
-
(2009)
Curr Biol : CB
, vol.19
, Issue.8
, pp. 706-712
-
-
Philippe, H.1
Derelle, R.2
Lopez, P.3
Pick, K.4
Borchiellini, C.5
Boury-Esnault, N.6
Vacelet, J.7
Renard, E.8
Houliston, E.9
QuEinnec, E.10
Da Silva, C.11
Wincker, P.12
Le Guyader, H.13
Leys, S.14
Jackson, D.J.15
Schreiber, F.16
Erpenbeck, D.17
Morgenstern, B.18
WOrheide, G.19
Manuel, M.20
more..
-
5
-
-
33644536713
-
Tunicates and not cephalochordates are the closest living relatives of vertebrates
-
10.1038/nature04336, 16495997
-
Delsuc F, Brinkmann H, Chourrout D, Philippe H. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 2006, 439(7079):965-968. [http://www.nature.com/doifinder/10.1038/nature04336], 10.1038/nature04336, 16495997.
-
(2006)
Nature
, vol.439
, Issue.7079
, pp. 965-968
-
-
Delsuc, F.1
Brinkmann, H.2
Chourrout, D.3
Philippe, H.4
-
6
-
-
46849087728
-
Phylogenetic Signal in the Eukaryotic Tree of Life
-
Sanderson MJ. Phylogenetic Signal in the Eukaryotic Tree of Life. Sci (New York, N.Y.) 2008, 321(5885):121-123. [http://www.sciencemag.org/cgi/doi/10.1126/science.1154449].
-
(2008)
Sci (New York, N.Y.)
, vol.321
, Issue.5885
, pp. 121-123
-
-
Sanderson, M.J.1
-
7
-
-
33749516796
-
Large-scale sequencing and the new animal phylogeny
-
10.1016/j.tree.2006.08.004, 16919363
-
Philippe H, Telford MJ. Large-scale sequencing and the new animal phylogeny. Trends Ecol Evol 2006, 21(11):614-620. [http://dx.doi.org/10.1016/j.tree.2006.08.004], 10.1016/j.tree.2006.08.004, 16919363.
-
(2006)
Trends Ecol Evol
, vol.21
, Issue.11
, pp. 614-620
-
-
Philippe, H.1
Telford, M.J.2
-
8
-
-
80052667788
-
Higher-level metazoan relationships: recent progress and remaining questions
-
Edgecombe GD, Giribet G, Dunn CW, Hejnol A, Kristensen RM, Neves RC, Rouse GW, Worsaae K, Sørensen MV. Higher-level metazoan relationships: recent progress and remaining questions. Org Divers Evol 2011, 11(2):151-172. [http://www.springerlink.com/index/10.1007/s13127-011-0044-4].
-
(2011)
Org Divers Evol
, vol.11
, Issue.2
, pp. 151-172
-
-
Edgecombe, G.D.1
Giribet, G.2
Dunn, C.W.3
Hejnol, A.4
Kristensen, R.M.5
Neves, R.C.6
Rouse, G.W.7
Worsaae, K.8
Sørensen, M.V.9
-
9
-
-
3142716808
-
PartiGene-constructing partial genomes
-
Parkinson J, Anthony A, Wasmuth J, Schmid R, Hedley A, Blaxter M. PartiGene-constructing partial genomes. Bioinformatics (Oxford, England) 2004, 20(9):1398-1404. [http://dx.doi.org/10.1093/bioinformatics/bth101].
-
(2004)
Bioinformatics (Oxford, England)
, vol.20
, Issue.9
, pp. 1398-1404
-
-
Parkinson, J.1
Anthony, A.2
Wasmuth, J.3
Schmid, R.4
Hedley, A.5
Blaxter, M.6
-
10
-
-
34248188251
-
SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics
-
Roure B, Rodriguez-Ezpeleta N, Philippe H. SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics. BMC Evol Biol 2007, 7(Suppl 1):S2. [http://www.biomedcentral.com/1471-2148/7/S1/S2].
-
(2007)
BMC Evol Biol
, vol.7
, Issue.SUPPL. 1
-
-
Roure, B.1
Rodriguez-Ezpeleta, N.2
Philippe, H.3
-
11
-
-
84888128914
-
BioLite, a lightweight bioinformatics framework with automated tracking of diagnostics and provenance
-
Boston, MA, USA
-
Howison M, Dunn CW, Sinnott-Armstrong NA. BioLite, a lightweight bioinformatics framework with automated tracking of diagnostics and provenance. Proceedings of the 4th USENIX Workshop on the Theory and Practice of Provenance (TaPP '12) 14-15 June 2012, Boston, MA, USA, https://www.usenix.org/system/files/conference/tapp12/tapp12-final5.pdf.
-
(2012)
Proceedings of the 4th USENIX Workshop on the Theory and Practice of Provenance (TaPP '12)
-
-
Howison, M.1
Dunn, C.W.2
Sinnott-Armstrong, N.A.3
-
12
-
-
65649092976
-
Biopython: freely available Python tools for computational molecular biology and bioinformatics
-
[PMID: 19304878], 10.1093/bioinformatics/btp163, 2682512, 19304878
-
Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, Hoon M. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009, 25(11):1422-1423. [http://bioinformatics.oxfordjournals.org/content/25/11/1422] [PMID: 19304878], 10.1093/bioinformatics/btp163, 2682512, 19304878.
-
(2009)
Bioinformatics
, vol.25
, Issue.11
, pp. 1422-1423
-
-
Cock, P.J.A.1
Antao, T.2
Chang, J.T.3
Chapman, B.A.4
Cox, C.J.5
Dalke, A.6
Friedberg, I.7
Hamelryck, T.8
Kauff, F.9
Wilczynski, B.10
Hoon, M.11
-
13
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
10.1038/nmeth.1923, 3322381, 22388286
-
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9(4):357-359. [http://www.nature.com/doifinder/10.1038/nmeth.1923], 10.1038/nmeth.1923, 3322381, 22388286.
-
(2012)
Nat Methods
, vol.9
, Issue.4
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
14
-
-
79960264362
-
Full-length transcriptome assembly from RNA-Seq data without a reference genome
-
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011,, [http://www.nature.com/doifinder/10.1038/nbt.1883].
-
(2011)
Nat Biotechnol
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
Levin, J.Z.4
Thompson, D.A.5
Amit, I.6
Adiconis, X.7
Fan, L.8
Raychowdhury, R.9
Zeng, Q.10
Chen, Z.11
Mauceli, E.12
Hacohen, N.13
Gnirke, A.14
Rhind, N.15
di Palma, F.16
Birren, B.W.17
Nusbaum, C.18
Lindblad-Toh, K.19
Friedman, N.20
Regev, A.21
more..
-
15
-
-
84856282851
-
FastQC: A quality control tool for high throughput sequence data
-
Andrews S. FastQC: A quality control tool for high throughput sequence data. [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/].
-
-
-
Andrews, S.1
-
16
-
-
79960264362
-
Full-length transcriptome assembly from RNA-Seq data without a reference genome
-
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotech 2011, 29(7):644-652.
-
(2011)
Nat Biotech
, vol.29
, Issue.7
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
Levin, J.Z.4
Thompson, D.A.5
Amit, I.6
Adiconis, X.7
Fan, L.8
Raychowdhury, R.9
Zeng, Q.10
Chen, Z.11
Mauceli, E.12
Hacohen, N.13
Gnirke, A.14
Rhind, N.15
di Palma, F.16
Birren, B.W.17
Nusbaum, C.18
Lindblad-Toh, K.19
Friedman, N.20
Regev, A.21
more..
-
17
-
-
84885406698
-
GNU Parallel: the command-line power tool
-
Tange O. GNU Parallel: the command-line power tool. Login 2011, 36:42-47. [https://www.usenix.org/publications/login/february-2011-volume-36-number-1/gnu-parallel-command-line-power-tool].
-
(2011)
Login
, vol.36
, pp. 42-47
-
-
Tange, O.1
-
18
-
-
79961123152
-
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
-
10.1186/1471-2105-12-323, 3163565, 21816040
-
Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 2011, 12:323. 10.1186/1471-2105-12-323, 3163565, 21816040.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 323
-
-
Li, B.1
Dewey, C.N.2
-
19
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
10.1093/nar/30.7.1575, 101833, 11917018
-
Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research 2002, 30(7):1575-1584. [http://dx.doi.org/10.1093/nar/30.7.1575], 10.1093/nar/30.7.1575, 101833, 11917018.
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.7
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
20
-
-
80052824121
-
MACSE: multiple alignment of coding SEquences accounting for frameshifts and stop codons
-
10.1371/journal.pone.0022594, 3174933, 21949676
-
Ranwez V, Harispe S, Delsuc F, Douzery EJP. MACSE: multiple alignment of coding SEquences accounting for frameshifts and stop codons. PLoS ONE 2011, 6(9):e22594. 10.1371/journal.pone.0022594, 3174933, 21949676.
-
(2011)
PLoS ONE
, vol.6
, Issue.9
-
-
Ranwez, V.1
Harispe, S.2
Delsuc, F.3
Douzery, E.J.P.4
-
21
-
-
34547489084
-
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
-
10.1080/10635150701472164, 17654362
-
Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 2007, 56(4):564-577. 10.1080/10635150701472164, 17654362.
-
(2007)
Syst Biol
, vol.56
, Issue.4
, pp. 564-577
-
-
Talavera, G.1
Castresana, J.2
-
22
-
-
33750403801
-
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (Oxford, England) 2006, 22(21):2688-2690.
-
(2006)
Bioinformatics (Oxford, England)
, vol.22
, Issue.21
, pp. 2688-2690
-
-
Stamatakis, A.1
-
23
-
-
84878113118
-
Inferring ancient divergences requires genes with strong phylogenetic signals
-
10.1038/nature12130, 23657258
-
Salichos L, Rokas A. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 2013, 497(7449):327-331. [http://dx.doi.org/10.1038/nature12130], 10.1038/nature12130, 23657258.
-
(2013)
Nature
, vol.497
, Issue.7449
, pp. 327-331
-
-
Salichos, L.1
Rokas, A.2
-
24
-
-
72749099971
-
Assessing the root of bilaterian animals with scalable phylogenomic methods
-
Hejnol A, Obst M, Stamatakis A, Ott M, Rouse GW, Edgecombe GD, Martinez P, Baguñà J, Bailly X, Jondelius U, Wiens M, Müller WEG, Seaver E, Wheeler WC, Martindale MQ, Giribet G, Dunn CW. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc Biol Sci / R Soc 2009, 276(1677):4261-4270. [http://dx.doi.org/10.1098/rspb.2009.0896].
-
(2009)
Proc Biol Sci / R Soc
, vol.276
, Issue.1677
, pp. 4261-4270
-
-
Hejnol, A.1
Obst, M.2
Stamatakis, A.3
Ott, M.4
Rouse, G.W.5
Edgecombe, G.D.6
Martinez, P.7
Baguñà, J.8
Bailly, X.9
Jondelius, U.10
Wiens, M.11
Müller, W.E.G.12
Seaver, E.13
Wheeler, W.C.14
Martindale, M.Q.15
Giribet, G.16
Dunn, C.W.17
-
25
-
-
77954202497
-
DendroPy: a Python library for phylogenetic computing
-
10.1093/bioinformatics/btq228, 20421198
-
Sukumaran J, Holder MT. DendroPy: a Python library for phylogenetic computing. Bioinformatics 2010, 26(12):1569-1571. [http://bioinformatics.oxfordjournals.org/content/26/12/1569], 10.1093/bioinformatics/btq228, 20421198.
-
(2010)
Bioinformatics
, vol.26
, Issue.12
, pp. 1569-1571
-
-
Sukumaran, J.1
Holder, M.T.2
-
26
-
-
84873326063
-
Genome-scale coestimation of species and gene trees
-
10.1101/gr.141978.112, 3561873, 23132911
-
Boussau B, Szollosi GJ, Duret L, Gouy M, Tannier E, Daubin V. Genome-scale coestimation of species and gene trees. Genome Res 2013, 23(2):323-330. [http://genome.cshlp.org/cgi/doi/10.1101/gr.141978.112], 10.1101/gr.141978.112, 3561873, 23132911.
-
(2013)
Genome Res
, vol.23
, Issue.2
, pp. 323-330
-
-
Boussau, B.1
Szollosi, G.J.2
Duret, L.3
Gouy, M.4
Tannier, E.5
Daubin, V.6
-
27
-
-
34447300950
-
Sea anemone genome reveals ancestral Eumetazoan gene repertoire and genomic organization
-
FINNERTY JR
-
Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, Technau U, Martindale MQ, Rokhsar DS, FINNERTY JR Sea anemone genome reveals ancestral Eumetazoan gene repertoire and genomic organization. Sci (New York, N.Y.) 2007, 317(5834):86-94. [http://www.sciencemag.org/cgi/doi/10.1126/science.1139158], FINNERTY JR.
-
(2007)
Sci (New York, N.Y.)
, vol.317
, Issue.5834
, pp. 86-94
-
-
Putnam, N.H.1
Srivastava, M.2
Hellsten, U.3
Dirks, B.4
Chapman, J.5
Salamov, A.6
Terry, A.7
Shapiro, H.8
Lindquist, E.9
Kapitonov, V.V.10
Jurka, J.11
Genikhovich, G.12
Grigoriev, I.V.13
Lucas, S.M.14
Steele, R.E.15
Technau, U.16
Martindale, M.Q.17
Rokhsar, D.S.18
-
28
-
-
77950080387
-
The dynamic genome of Hydra
-
10.1038/nature08830, 20228792
-
Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T, Balasubramanian PG, Borman J, Busam D, Disbennett K, Pfannkoch C, Sumin N, Sutton GG, Viswanathan LD, Walenz B, Goodstein DM, Hellsten U, Kawashima T, Prochnik SE, Putnam NH, Shu S, Blumberg B, Dana CE, Gee L, Kibler DF, Law L, Lindgens D, Martinez DE, Peng J, et al. The dynamic genome of Hydra. Nature 2010, 464(7288):592-596. [http://dx.doi.org/10.1038/nature08830], 10.1038/nature08830, 20228792.
-
(2010)
Nature
, vol.464
, Issue.7288
, pp. 592-596
-
-
Chapman, J.A.1
Kirkness, E.F.2
Simakov, O.3
Hampson, S.E.4
Mitros, T.5
Weinmaier, T.6
Rattei, T.7
Balasubramanian, P.G.8
Borman, J.9
Busam, D.10
Disbennett, K.11
Pfannkoch, C.12
Sumin, N.13
Sutton, G.G.14
Viswanathan, L.D.15
Walenz, B.16
Goodstein, D.M.17
Hellsten, U.18
Kawashima, T.19
Prochnik, S.E.20
Putnam, N.H.21
Shu, S.22
Blumberg, B.23
Dana, C.E.24
Gee, L.25
Kibler, D.F.26
Law, L.27
Lindgens, D.28
Martinez, D.E.29
Peng, J.30
more..
-
29
-
-
28444437795
-
Molecular Phylogenetics of the Siphonophora (Cnidaria), with implications for the evolution of functional specialization
-
10.1080/10635150500354837, 16338764
-
Dunn C, Pugh P, Haddock S. Molecular Phylogenetics of the Siphonophora (Cnidaria), with implications for the evolution of functional specialization. Syst Biol 2005, 54(6):916-935. [http://sysbio.oxfordjournals.org/cgi/doi/10.1080/10635150500354837], 10.1080/10635150500354837, 16338764.
-
(2005)
Syst Biol
, vol.54
, Issue.6
, pp. 916-935
-
-
Dunn, C.1
Pugh, P.2
Haddock, S.3
-
30
-
-
37849023306
-
Assessing performance of orthology detection strategies applied to eukaryotic genomes
-
10.1371/journal.pone.0000383, 1849888, 17440619
-
Chen F, Mackey AJ, Vermunt JK, Roos DS. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS ONE 2007, 2(4):e383. [http://dx.plos.org/10.1371/journal.pone.0000383], 10.1371/journal.pone.0000383, 1849888, 17440619.
-
(2007)
PLoS ONE
, vol.2
, Issue.4
-
-
Chen, F.1
Mackey, A.J.2
Vermunt, J.K.3
Roos, D.S.4
-
31
-
-
84872287798
-
Inferring hierarchical orthologous groups from orthologous gene pairs
-
10.1371/journal.pone.0053786, 3544860, 23342000
-
Altenhoff AM, Gil M, Gonnet GH, Dessimoz C. Inferring hierarchical orthologous groups from orthologous gene pairs. PLoS ONE 2013, 8:e53786. [http://dx.doi.org/10.1371/journal.pone.0053786], 10.1371/journal.pone.0053786, 3544860, 23342000.
-
(2013)
PLoS ONE
, vol.8
-
-
Altenhoff, A.M.1
Gil, M.2
Gonnet, G.H.3
Dessimoz, C.4
|