-
1
-
-
20744436518
-
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases
-
10.1093/bioinformatics/bti325, 15713731
-
Dufayard JF, Duret L, Penel S, Gouy M, Rechenmann F, Perrière G. Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics 2005, 21:2596-2603. 10.1093/bioinformatics/bti325, 15713731.
-
(2005)
Bioinformatics
, vol.21
, pp. 2596-2603
-
-
Dufayard, J.F.1
Duret, L.2
Penel, S.3
Gouy, M.4
Rechenmann, F.5
Perrière, G.6
-
2
-
-
74049118261
-
Large-scale assignment of orthology: back to phylogenetics?
-
10.1186/gb-2008-9-10-235, 2760865, 18983710
-
Gabaldón T. Large-scale assignment of orthology: back to phylogenetics?. Genome Biol 2008, 9:235. 10.1186/gb-2008-9-10-235, 2760865, 18983710.
-
(2008)
Genome Biol
, vol.9
, pp. 235
-
-
Gabaldón, T.1
-
3
-
-
59149102602
-
Phylogenetic and functional assessment of orthologs inference projects and methods
-
10.1371/journal.pcbi.1000262, 2612752, 19148271
-
Altenhoff AM, Dessimoz C. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol 2009, 5:e1000262. 10.1371/journal.pcbi.1000262, 2612752, 19148271.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Altenhoff, A.M.1
Dessimoz, C.2
-
4
-
-
78651277241
-
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score
-
3061081, 21149260
-
Pryszcz LP, Huerta-Cepas J, Gabaldón T. MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. Nucleic Acids Res 2010, 39:e32. 3061081, 21149260.
-
(2010)
Nucleic Acids Res
, vol.39
-
-
Pryszcz, L.P.1
Huerta-Cepas, J.2
Gabaldón, T.3
-
5
-
-
77954843377
-
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests
-
10.1186/1471-2105-11-324, 2905365, 20550700
-
Abby SS, Tannier E, Gouy M, Daubin V. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. BMC Bioinformatics 2010, 11:324. 10.1186/1471-2105-11-324, 2905365, 20550700.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 324
-
-
Abby, S.S.1
Tannier, E.2
Gouy, M.3
Daubin, V.4
-
6
-
-
50649104620
-
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes
-
10.1101/gr.076992.108, 2527703, 18562677
-
Studer RA, Penel S, Duret L, Robinson-Rechavi M. Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res 2008, 18:1393-1402. 10.1101/gr.076992.108, 2527703, 18562677.
-
(2008)
Genome Res
, vol.18
, pp. 1393-1402
-
-
Studer, R.A.1
Penel, S.2
Duret, L.3
Robinson-Rechavi, M.4
-
7
-
-
17244367011
-
Homology-dependent methylation in primate repetitive DNA
-
10.1073/pnas.0408986102, 556223, 15797989
-
Meunier J, Khelifi A, Navratil V, Duret L. Homology-dependent methylation in primate repetitive DNA. Proc Natl Acad Sci USA 2005, 102:5471-5476. 10.1073/pnas.0408986102, 556223, 15797989.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 5471-5476
-
-
Meunier, J.1
Khelifi, A.2
Navratil, V.3
Duret, L.4
-
8
-
-
2942684863
-
The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny
-
10.1007/s00239-004-2587-x, 15461422
-
Belle EM, Duret L, Galtier N, Eyre-Walker A. The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny. J Mol Evol 2004, 58:653-660. 10.1007/s00239-004-2587-x, 15461422.
-
(2004)
J Mol Evol
, vol.58
, pp. 653-660
-
-
Belle, E.M.1
Duret, L.2
Galtier, N.3
Eyre-Walker, A.4
-
9
-
-
67649115335
-
Databases of homologous gene families for comparative genomics
-
10.1186/1471-2105-10-S6-S3, 2788354, 19958513
-
Penel S, Arigon AM, Dufayard JF, Sertier AS, Daubin V, Duret L, Gouy M, Perrière G. Databases of homologous gene families for comparative genomics. BMC Bioinformatics 2009, 10(Suppl 6):S3. 10.1186/1471-2105-10-S6-S3, 2788354, 19958513.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL. 6
-
-
Penel, S.1
Arigon, A.M.2
Dufayard, J.F.3
Sertier, A.S.4
Daubin, V.5
Duret, L.6
Gouy, M.7
Perrière, G.8
-
10
-
-
33745955637
-
Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics
-
10.1186/1471-2105-7-188, 1501049, 16594991
-
Dutheil J, Gaillard S, Bazin E, Glemin S, Ranwez V, Galtier N, Belkhir K. Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. BMC Bioinformatics 2006, 7:188. 10.1186/1471-2105-7-188, 1501049, 16594991.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 188
-
-
Dutheil, J.1
Gaillard, S.2
Bazin, E.3
Glemin, S.4
Ranwez, V.5
Galtier, N.6
Belkhir, K.7
-
11
-
-
84864346710
-
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
-
10.1098/rspb.2012.0683, 22628470, Yang Z
-
Dos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PCJ, Yang Z Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc R Soc B 2012, 279:3491-3500. 10.1098/rspb.2012.0683, 22628470, Yang Z.
-
(2012)
Proc R Soc B
, vol.279
, pp. 3491-3500
-
-
Dos Reis, M.1
Inoue, J.2
Hasegawa, M.3
Asher, R.J.4
Donoghue, P.C.J.5
-
12
-
-
0033759527
-
The comparison of beta-thymosin homologues among metazoa supports an arthropod-nematode clade
-
Manuel M, Kruse M, Muller WE, Le Parco Y. The comparison of beta-thymosin homologues among metazoa supports an arthropod-nematode clade. J Mol Evol 2000, 51:378-381.
-
(2000)
J Mol Evol
, vol.51
, pp. 378-381
-
-
Manuel, M.1
Kruse, M.2
Muller, W.E.3
Le Parco, Y.4
-
13
-
-
0037143719
-
A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians
-
10.1073/pnas.172390199, 123241, 12177440
-
Ruiz-Trillo I, Paps J, Loukota M, Ribera C, Jondelius U, Baguna J, Riutort M. A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians. Proc Natl Acad Sci USA 2002, 99:11246-11251. 10.1073/pnas.172390199, 123241, 12177440.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 11246-11251
-
-
Ruiz-Trillo, I.1
Paps, J.2
Loukota, M.3
Ribera, C.4
Jondelius, U.5
Baguna, J.6
Riutort, M.7
-
14
-
-
0036184428
-
Testing the new animal phylogeny: first use of combined large-subunit and small-subunit rRNA gene sequences to classify the protostomes
-
10.1093/oxfordjournals.molbev.a004082, 11861888
-
Mallatt J, Winchell CJ. Testing the new animal phylogeny: first use of combined large-subunit and small-subunit rRNA gene sequences to classify the protostomes. Mol Biol Evol 2002, 19:289-301. 10.1093/oxfordjournals.molbev.a004082, 11861888.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 289-301
-
-
Mallatt, J.1
Winchell, C.J.2
-
15
-
-
0344952061
-
The evolutionary position of nematodes
-
10.1186/1471-2148-2-7, 102755, 11985779
-
Blair JE, Ikeo K, Gojobori T, Hedges SB. The evolutionary position of nematodes. BMC Evol Biol 2002, 2:7. 10.1186/1471-2148-2-7, 102755, 11985779.
-
(2002)
BMC Evol Biol
, vol.2
, pp. 7
-
-
Blair, J.E.1
Ikeo, K.2
Gojobori, T.3
Hedges, S.B.4
-
16
-
-
0345874732
-
Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis
-
314272, 14707168
-
Wolf YI, Rogozin IB, Koonin EV. Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res 2004, 14:29-36. 314272, 14707168.
-
(2004)
Genome Res
, vol.14
, pp. 29-36
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Koonin, E.V.3
-
17
-
-
35848952076
-
Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation
-
10.1093/molbev/msm207, 17893400
-
Zheng J, Rogozin IB, Koonin EV, Przytycka TM. Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation. Mol Biol Evol 2007, 24:2583-2592. 10.1093/molbev/msm207, 17893400.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 2583-2592
-
-
Zheng, J.1
Rogozin, I.B.2
Koonin, E.V.3
Przytycka, T.M.4
-
18
-
-
27844438226
-
Genome-scale evidence of the nematode-arthropod clade
-
10.1186/gb-2005-6-5-r41, 1175953, 15892869
-
Dopazo H, Dopazo J. Genome-scale evidence of the nematode-arthropod clade. Genome Biol 2005, 6:R41. 10.1186/gb-2005-6-5-r41, 1175953, 15892869.
-
(2005)
Genome Biol
, vol.6
-
-
Dopazo, H.1
Dopazo, J.2
-
19
-
-
40549115956
-
Improvement of molecular phylogenetic inference and the phylogeny of Bilateria
-
Lartillot N, Philippe H. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Philos Trans R Soc B 2008, 363:1463-1472.
-
(2008)
Philos Trans R Soc B
, vol.363
, pp. 1463-1472
-
-
Lartillot, N.1
Philippe, H.2
-
20
-
-
77958450862
-
Deep genomic-scale analyses of the metazoa reject Coelomata: evidence from single- and multigene families analyzed under a supertree and supermatrix paradigm
-
10.1093/gbe/evq016, 2997542, 20624736
-
Holton TA, Pisani D. Deep genomic-scale analyses of the metazoa reject Coelomata: evidence from single- and multigene families analyzed under a supertree and supermatrix paradigm. Genome Biol Evol 2010, 2:310-324. 10.1093/gbe/evq016, 2997542, 20624736.
-
(2010)
Genome Biol Evol
, vol.2
, pp. 310-324
-
-
Holton, T.A.1
Pisani, D.2
-
21
-
-
3943059570
-
High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome
-
10.1038/nature02697, 15295601
-
Denver DR, Morris K, Lynch M, Thomas WK. High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature 2004, 430:679-682. 10.1038/nature02697, 15295601.
-
(2004)
Nature
, vol.430
, pp. 679-682
-
-
Denver, D.R.1
Morris, K.2
Lynch, M.3
Thomas, W.K.4
-
22
-
-
0141609706
-
Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, γ-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models
-
10.1016/S1055-7903(03)00115-5, 12878459
-
Waddell PJ, Shelley S. Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, γ-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models. Mol Phylogenet Evol 2003, 28:197-224. 10.1016/S1055-7903(03)00115-5, 12878459.
-
(2003)
Mol Phylogenet Evol
, vol.28
, pp. 197-224
-
-
Waddell, P.J.1
Shelley, S.2
-
23
-
-
74249106740
-
PhyloPattern: regular expression to identify complex patterns in phylogenetic trees
-
10.1186/1471-2105-10-298, 2759962, 19765311
-
Gouret P, Thompson JD, Pontarotti P. PhyloPattern: regular expression to identify complex patterns in phylogenetic trees. BMC Bioinformatics 2009, 10:298. 10.1186/1471-2105-10-298, 2759962, 19765311.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 298
-
-
Gouret, P.1
Thompson, J.D.2
Pontarotti, P.3
-
24
-
-
0027759230
-
So, what about the molecular clock hypothesis?
-
10.1016/0959-437X(93)90011-D, 8118215
-
Li WH. So, what about the molecular clock hypothesis?. Curr Opin Genet Dev 1993, 3:896-901. 10.1016/0959-437X(93)90011-D, 8118215.
-
(1993)
Curr Opin Genet Dev
, vol.3
, pp. 896-901
-
-
Li, W.H.1
-
25
-
-
0031949306
-
Duplication-based measures of difference between gene and species trees
-
10.1089/cmb.1998.5.135, 9541877
-
Eulenstein O, Mirkin B, Vingron M. Duplication-based measures of difference between gene and species trees. J Comput Biol 1998, 5:135-148. 10.1089/cmb.1998.5.135, 9541877.
-
(1998)
J Comput Biol
, vol.5
, pp. 135-148
-
-
Eulenstein, O.1
Mirkin, B.2
Vingron, M.3
-
26
-
-
84877152040
-
Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem
-
10.1186/1471-2105-13-S10-S14, 3521216, 23282138
-
Górecki P, Eulenstein O. Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem. BMC Bioinformatics 2012, 13(Suppl 10):S14. 10.1186/1471-2105-13-S10-S14, 3521216, 23282138.
-
(2012)
BMC Bioinformatics
, vol.13
, Issue.SUPPL. 10
-
-
Górecki, P.1
Eulenstein, O.2
-
27
-
-
41149083635
-
Remote access to ACNUC nucleotide and protein sequence databases at PBIL
-
10.1016/j.biochi.2007.07.003, 17825976
-
Gouy M, Delmotte S. Remote access to ACNUC nucleotide and protein sequence databases at PBIL. Biochimie 2008, 90:555-562. 10.1016/j.biochi.2007.07.003, 17825976.
-
(2008)
Biochimie
, vol.90
, pp. 555-562
-
-
Gouy, M.1
Delmotte, S.2
|