-
1
-
-
0030902563
-
Phylogenetic Methods Come of Age: Testing Hypotheses in an Evolutionary Context
-
Huelsenbeck J, Rannala B. Phylogenetic Methods Come of Age: Testing Hypotheses in an Evolutionary Context. Science 1997, 276:227-232.
-
(1997)
Science
, vol.276
, pp. 227-232
-
-
Huelsenbeck, J.1
Rannala, B.2
-
2
-
-
38849149795
-
28-way vertebrate alignment and conservation track in the UCSC genome browser
-
2099589, 17984227
-
Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King D, Baertsch R, Blankenberg D, Pond SK, Nekrutenko A, Giardine B, Harris R, Tyekucheva S, Diekhans M, Pringle T, Murphy W, Lesk A, Weinstock G, Lindblad-Toh K, Gibbs R, Lander E, Siepel A, Haussler D, Kent W. 28-way vertebrate alignment and conservation track in the UCSC genome browser. Genome Res. 2007, 17:1797-1808. 2099589, 17984227.
-
(2007)
Genome Res.
, vol.17
, pp. 1797-1808
-
-
Miller, W.1
Rosenbloom, K.2
Hardison, R.C.3
Hou, M.4
Taylor, J.5
Raney, B.6
Burhans, R.7
King, D.8
Baertsch, R.9
Blankenberg, D.10
Pond, S.K.11
Nekrutenko, A.12
Giardine, B.13
Harris, R.14
Tyekucheva, S.15
Diekhans, M.16
Pringle, T.17
Murphy, W.18
Lesk, A.19
Weinstock, G.20
Lindblad-Toh, K.21
Gibbs, R.22
Lander, E.23
Siepel, A.24
Haussler, D.25
Kent, W.26
more..
-
3
-
-
34548743476
-
Gene conversion: mechanisms, evolution and human disease
-
Chen J, Cooper D, Chuzhanova N, Ferec C, Patrinos G. Gene conversion: mechanisms, evolution and human disease. Nature Reviews Genetics 2007, 8:762-775.
-
(2007)
Nature Reviews Genetics
, vol.8
, pp. 762-775
-
-
Chen, J.1
Cooper, D.2
Chuzhanova, N.3
Ferec, C.4
Patrinos, G.5
-
4
-
-
0027471670
-
A Heuristic Method to Reconstruct the History of Sequences Subject to Recombination
-
Hein J. A Heuristic Method to Reconstruct the History of Sequences Subject to Recombination. J. Mol. Evol. 1993, 36:396-405.
-
(1993)
J. Mol. Evol.
, vol.36
, pp. 396-405
-
-
Hein, J.1
-
5
-
-
0031041347
-
A likelihood method for the detection of selection and recombination using nucleotide sequences
-
Grassly N, Holmes E. A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol. Biol. Evol. 1997, 14:239-247.
-
(1997)
Mol. Biol. Evol.
, vol.14
, pp. 239-247
-
-
Grassly, N.1
Holmes, E.2
-
6
-
-
0033021298
-
Phylogenetic Evidence for Recombination in Dengue Virus
-
Holmes E, Worobey M, Rambaut A. Phylogenetic Evidence for Recombination in Dengue Virus. Mol. Biol. Evol. 1999, 16:405-409.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 405-409
-
-
Holmes, E.1
Worobey, M.2
Rambaut, A.3
-
7
-
-
0036301764
-
Gene conversion and the evolution of euryarchaeal chaperonins: a maximum likelihood-based method for detecting conflicting phylogenetic signals
-
Archibald J, Roger A. Gene conversion and the evolution of euryarchaeal chaperonins: a maximum likelihood-based method for detecting conflicting phylogenetic signals. J. Mol. Evol. 2002, 55:232-245.
-
(2002)
J. Mol. Evol.
, vol.55
, pp. 232-245
-
-
Archibald, J.1
Roger, A.2
-
8
-
-
33748770095
-
Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm
-
Pond S, Posada D, Gravenor M, Woelk C, Frost S. Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm. Mol. Biol. Evol. 2006, 23:1891-1901.
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 1891-1901
-
-
Pond, S.1
Posada, D.2
Gravenor, M.3
Woelk, C.4
Frost, S.5
-
9
-
-
0033753825
-
Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences
-
Gibbs M, Armstrong J, Gibbs A. Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 2000, 16:573-582.
-
(2000)
Bioinformatics
, vol.16
, pp. 573-582
-
-
Gibbs, M.1
Armstrong, J.2
Gibbs, A.3
-
10
-
-
0042243482
-
Inferring spatial phylogenetic variation along nucleotie sequences: A multiple changepoint model
-
Suchard M, Weiss R, Dorman K, Sinsheimer J. Inferring spatial phylogenetic variation along nucleotie sequences: A multiple changepoint model. J. Am. Stat. Assoc. 2003, 98:427-437.
-
(2003)
J. Am. Stat. Assoc.
, vol.98
, pp. 427-437
-
-
Suchard, M.1
Weiss, R.2
Dorman, K.3
Sinsheimer, J.4
-
11
-
-
21444455535
-
Dual multiple change-point model leads to more accurate recombination detection
-
Minin V, Dorman K, Fang F, Suchard M. Dual multiple change-point model leads to more accurate recombination detection. Bioinformatics 2005, 21:3034-3042.
-
(2005)
Bioinformatics
, vol.21
, pp. 3034-3042
-
-
Minin, V.1
Dorman, K.2
Fang, F.3
Suchard, M.4
-
12
-
-
27544493059
-
Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models
-
Husmeier D. Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models. Bioinformatics 2005, 21:ii166-ii172.
-
(2005)
Bioinformatics
, vol.21
-
-
Husmeier, D.1
-
13
-
-
63549098393
-
Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments
-
2651022, 19300487
-
Westesson O, Holmes I. Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments. PLoS Comput. Biol. 2009, 5:e1000318. 2651022, 19300487.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Westesson, O.1
Holmes, I.2
-
14
-
-
0024356449
-
Statistical tests for detecting gene conversion
-
Sawyer S. Statistical tests for detecting gene conversion. Mol. Biol. Evol. 1989, 6:526-538.
-
(1989)
Mol. Biol. Evol.
, vol.6
, pp. 526-538
-
-
Sawyer, S.1
-
15
-
-
84888283600
-
Analyzing the mosaic structure of genes
-
Smith J. Analyzing the mosaic structure of genes. Mol. Biol. Evol. 1992, 16:1369-1390.
-
(1992)
Mol. Biol. Evol.
, vol.16
, pp. 1369-1390
-
-
Smith, J.1
-
16
-
-
0024356449
-
Statistical tests for detecting gene conversion
-
Siepel A, Korber B. Statistical tests for detecting gene conversion. Mol. Biol. Evol. 1995, 6:526-538.
-
(1995)
Mol. Biol. Evol.
, vol.6
, pp. 526-538
-
-
Siepel, A.1
Korber, B.2
-
17
-
-
0032889281
-
Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-InfecteSeroconverters in India, with Evidence of Intersubtype Recombination
-
Lole K, Bollinger R, Paranjape R, Gadkari D, Kulkarni S, Novak N, Ingersoll R, Sheppard H, Ray S. Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-InfecteSeroconverters in India, with Evidence of Intersubtype Recombination. J Virol 1999, 73:152-160.
-
(1999)
J Virol
, vol.73
, pp. 152-160
-
-
Lole, K.1
Bollinger, R.2
Paranjape, R.3
Gadkari, D.4
Kulkarni, S.5
Novak, N.6
Ingersoll, R.7
Sheppard, H.8
Ray, S.9
-
18
-
-
0035923699
-
Evaluation of methods for detecting recombination from DNA sequences Computer simulations
-
61114, 11717435
-
Posada D, Crandall K. Evaluation of methods for detecting recombination from DNA sequences Computer simulations. PNAS 98:13757-13762. 61114, 11717435.
-
PNAS
, vol.98
, pp. 13757-13762
-
-
Posada, D.1
Crandall, K.2
-
19
-
-
13144283628
-
A Modified Bootscan Algorithm for Automated Identification of Recombinant Sequences and Recombination Breakpoints
-
Martin D, Posada D, Crandall K, Williamson C. A Modified Bootscan Algorithm for Automated Identification of Recombinant Sequences and Recombination Breakpoints. AIDS Res. Hum. Retroviruses 2005, 21:98-102.
-
(2005)
AIDS Res. Hum. Retroviruses
, vol.21
, pp. 98-102
-
-
Martin, D.1
Posada, D.2
Crandall, K.3
Williamson, C.4
-
20
-
-
34250757252
-
An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets
-
1894573, 17409078
-
Boni M, Posada D, Feldman M. An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets. Genetics 2007, 176:1035-1047. 1894573, 17409078.
-
(2007)
Genetics
, vol.176
, pp. 1035-1047
-
-
Boni, M.1
Posada, D.2
Feldman, M.3
-
21
-
-
52949114578
-
Identifying the Important HIV-1 Recombination Breakpoints
-
2522274, 18787691
-
Archer J, Pinney J, Fan J, Simon-Loriere E, Arts E, Negroni M, Robertson D. Identifying the Important HIV-1 Recombination Breakpoints. PLoS. Comput. Biol. 2008, 4:e1000178. 2522274, 18787691.
-
(2008)
PLoS. Comput. Biol.
, vol.4
-
-
Archer, J.1
Pinney, J.2
Fan, J.3
Simon-Loriere, E.4
Arts, E.5
Negroni, M.6
Robertson, D.7
-
22
-
-
78651235606
-
Whole-Genome Analysis of Gene Conversion Events
-
Budapest, Hungary, Ciccarelli F, Miklos I
-
Hsu C, Zhang Y, Hardison R, Miller W. Whole-Genome Analysis of Gene Conversion Events. Proceedings of RECOMB Comparative Genomics 2009 2009, 181-192. Budapest, Hungary, Ciccarelli F, Miklos I.
-
(2009)
Proceedings of RECOMB Comparative Genomics 2009
, pp. 181-192
-
-
Hsu, C.1
Zhang, Y.2
Hardison, R.3
Miller, W.4
-
23
-
-
13444251528
-
RDP2: recombination detection and analysis from sequence alignments
-
Martin D, Williamson C, Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 2005, 21:260-262.
-
(2005)
Bioinformatics
, vol.21
, pp. 260-262
-
-
Martin, D.1
Williamson, C.2
Posada, D.3
-
24
-
-
0036097812
-
Evaluation of Methods for Detecting Recombination from DNA sequences: Empirical Data
-
Posada D. Evaluation of Methods for Detecting Recombination from DNA sequences: Empirical Data. Mol. Biol. Evol. 19:708-717.
-
Mol. Biol. Evol.
, vol.19
, pp. 708-717
-
-
Posada, D.1
-
25
-
-
77749261529
-
The Power of the Methods for Detecting Interlocus Gene Conversion
-
2828729, 19948889
-
Mansai S, Innan H. The Power of the Methods for Detecting Interlocus Gene Conversion. Genetics 184:517-527. 2828729, 19948889.
-
Genetics
, vol.184
, pp. 517-527
-
-
Mansai, S.1
Innan, H.2
-
26
-
-
0034491799
-
SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography
-
Excoffier L, Novembre J, Schneider S. SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography. J. Hered. 2000, 91:506-509.
-
(2000)
J. Hered.
, vol.91
, pp. 506-509
-
-
Excoffier, L.1
Novembre, J.2
Schneider, S.3
-
27
-
-
0036184745
-
Generating samples under a Wright-Fisher neutral model of genetic variation
-
Hudson R. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 2002, 18:337-338.
-
(2002)
Bioinformatics
, vol.18
, pp. 337-338
-
-
Hudson, R.1
-
28
-
-
0037314075
-
Simulating haplotype blocks in the human genome
-
Posada D, Wiuf C. Simulating haplotype blocks in the human genome. Bioinformatics 2003, 19:289-290.
-
(2003)
Bioinformatics
, vol.19
, pp. 289-290
-
-
Posada, D.1
Wiuf, C.2
-
29
-
-
4644333804
-
SelSim: a program to simulate population genetic data with natural selection and recombination
-
Spencer C, Coop G. SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics 2004, 20:3673-3675.
-
(2004)
Bioinformatics
, vol.20
, pp. 3673-3675
-
-
Spencer, C.1
Coop, G.2
-
30
-
-
27644455774
-
CoaSim: a flexible environment for simulating genetic data under coalescent models
-
1274299, 16225674
-
Mailund T, Schierup M, Pedersen C, Mechlenborg P, Madsen J, Schauser L. CoaSim: a flexible environment for simulating genetic data under coalescent models. BMC Bioinformatics 2005, 6:252. 1274299, 16225674.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 252
-
-
Mailund, T.1
Schierup, M.2
Pedersen, C.3
Mechlenborg, P.4
Madsen, J.5
Schauser, L.6
-
31
-
-
27544497650
-
Calibrating a coalescent simulation of human genome sequence variation
-
1310645, 16251467
-
Schaffner S, Foo C, Gabriel S, Reich D, Daly M, Altshuler D. Calibrating a coalescent simulation of human genome sequence variation. Genome Res. 2005, 15:1576-1583. 1310645, 16251467.
-
(2005)
Genome Res.
, vol.15
, pp. 1576-1583
-
-
Schaffner, S.1
Foo, C.2
Gabriel, S.3
Reich, D.4
Daly, M.5
Altshuler, D.6
-
32
-
-
33646348730
-
Fast " coalescent" simulation
-
1458357, 16539698
-
Marjoram P, Wall J. Fast " coalescent" simulation. BMC Genet. 2006, 7:16. 1458357, 16539698.
-
(2006)
BMC Genet.
, vol.7
, pp. 16
-
-
Marjoram, P.1
Wall, J.2
-
33
-
-
38349167557
-
Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography
-
2206059, 18028540
-
Arenas M, Posada D. Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography. BMC Bioinformatics 2007, 8:458. 2206059, 18028540.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 458
-
-
Arenas, M.1
Posada, D.2
-
34
-
-
33847273741
-
MsHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots
-
Hellenthal G, Stephens M. msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots. Bioinformatics 2007, 23:520-521.
-
(2007)
Bioinformatics
, vol.23
, pp. 520-521
-
-
Hellenthal, G.1
Stephens, M.2
-
35
-
-
34547830810
-
GENOME: a rapid coalescent-based whole genome simulator
-
Liang L, Zollner S, Abecasis G. GENOME: a rapid coalescent-based whole genome simulator. Bioinformatics 2007, 23:1565-1567.
-
(2007)
Bioinformatics
, vol.23
, pp. 1565-1567
-
-
Liang, L.1
Zollner, S.2
Abecasis, G.3
-
36
-
-
77749261568
-
Coalescent Simulation of Intracodon Recombination
-
2828723, 19933876
-
Arenas M, Posada D. Coalescent Simulation of Intracodon Recombination. Genetics 2010, 184:429-437. 2828723, 19933876.
-
(2010)
Genetics
, vol.184
, pp. 429-437
-
-
Arenas, M.1
Posada, D.2
-
38
-
-
28544438123
-
MySSP: non-stationary evolutionary sequence simulation, including indels
-
2658873, 19325855
-
Rosenberg M. MySSP: non-stationary evolutionary sequence simulation, including indels. Evol. Bioinform. Online 2005, 1:81-83. 2658873, 19325855.
-
(2005)
Evol. Bioinform. Online
, vol.1
, pp. 81-83
-
-
Rosenberg, M.1
-
39
-
-
28944454501
-
DNA assembly with gaps (Dawg): simulating sequence evolution
-
Cartwright R. DNA assembly with gaps (Dawg): simulating sequence evolution. Bioinformatics 2005, 21:iii31-38.
-
(2005)
Bioinformatics
, vol.21
-
-
Cartwright, R.1
-
40
-
-
73349096292
-
Biological Sequence Simulation for Testing Complex Evolutionary Hypotheses: indel-Seq-Gen Version 2.0
-
2760465, 19651852
-
Strope C, Abel K, Scott S, Moriyama E. Biological Sequence Simulation for Testing Complex Evolutionary Hypotheses: indel-Seq-Gen Version 2.0. Mol. Biol. Evol. 2009, 26:2581-2593. 2760465, 19651852.
-
(2009)
Mol. Biol. Evol.
, vol.26
, pp. 2581-2593
-
-
Strope, C.1
Abel, K.2
Scott, S.3
Moriyama, E.4
-
41
-
-
76949098763
-
Towards realistic benchmarks for multiple alignments of non-coding sequences
-
2823711, 20102627
-
Kim J, Sinha S. Towards realistic benchmarks for multiple alignments of non-coding sequences. BMC Bioinformatics 2010, 11:54. 2823711, 20102627.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 54
-
-
Kim, J.1
Sinha, S.2
-
42
-
-
77953826984
-
Improved pairwise alignment of genomic DNA
-
Pennsylvania State University
-
Harris R. Improved pairwise alignment of genomic DNA. PhD thesis 2007, Pennsylvania State University.
-
(2007)
PhD thesis
-
-
Harris, R.1
-
43
-
-
0022376704
-
Dating the human-ape splitting by a molecular clock of mitochondrial DNA
-
Hasegawa M, Kishimo M, Yano T. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 1985, 22:160-174.
-
(1985)
J. Mol. Evol.
, vol.22
, pp. 160-174
-
-
Hasegawa, M.1
Kishimo, M.2
Yano, T.3
-
44
-
-
47249087729
-
Reconstructing the evolutionary history of complex human gene clusters
-
Singapore, Vingron M, Wong L
-
Zhang Y, Song G, Vinar T, Green E, Siepel A, Miller W. Reconstructing the evolutionary history of complex human gene clusters. Proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2008) 2008, 29-49. Singapore, Vingron M, Wong L.
-
(2008)
Proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2008)
, pp. 29-49
-
-
Zhang, Y.1
Song, G.2
Vinar, T.3
Green, E.4
Siepel, A.5
Miller, W.6
-
45
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel A, Bejerano G, Pedersen J, Hinrichs A, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier L, Richards S, Weinstock G, Wilson R, Gibbs R, Kent W, Miller W, D H. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2006, 15:167-172.
-
(2006)
Genome Res.
, vol.15
, pp. 167-172
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.3
Hinrichs, A.4
Hou, M.5
Rosenbloom, K.6
Clawson, H.7
Spieth, J.8
Hillier, L.9
Richards, S.10
Weinstock, G.11
Wilson, R.12
Gibbs, R.13
Kent, W.14
Miller, W.15
D, H.16
|