-
1
-
-
65649131928
-
Gene tree discordance, phylogenetic inference, and the multispecies coalescent
-
10.1016/j.tree.2009.01.009, 19307040
-
Degnan JH, Rosenberg NA. Gene tree discordance, phylogenetic inference, and the multispecies coalescent. Trends Ecol Evol 2009, 24:332-340. 10.1016/j.tree.2009.01.009, 19307040.
-
(2009)
Trends Ecol Evol
, vol.24
, pp. 332-340
-
-
Degnan, J.H.1
Rosenberg, N.A.2
-
2
-
-
33646928341
-
Discordance of species trees with their most likely gene trees
-
Degnan JH, Rosenberg NA. Discordance of species trees with their most likely gene trees. PLoS Genet 2006, 2:762-768.
-
(2006)
PLoS Genet
, vol.2
, pp. 762-768
-
-
Degnan, J.H.1
Rosenberg, N.A.2
-
3
-
-
33644606488
-
Inferring phylogeny despite incomplete lineage sorting
-
10.1080/10635150500354928, 16507521
-
Maddison WP, Knowles LL. Inferring phylogeny despite incomplete lineage sorting. Syst Biol 2006, 55:21-30. 10.1080/10635150500354928, 16507521.
-
(2006)
Syst Biol
, vol.55
, pp. 21-30
-
-
Maddison, W.P.1
Knowles, L.L.2
-
4
-
-
70349658769
-
Species tree inference by minimizing deep coalescences
-
10.1371/journal.pcbi.1000501, 2729383, 19749978
-
Than C, Nakhleh L. Species tree inference by minimizing deep coalescences. PLoS Comput Biol 2009, 5:e1000501. 10.1371/journal.pcbi.1000501, 2729383, 19749978.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Than, C.1
Nakhleh, L.2
-
5
-
-
70349425459
-
Estimating species phylogenies using coalescence times among sequences
-
10.1093/sysbio/syp031, 20525601
-
Liu L, Yu L, Pearl DK, Edwards SV. Estimating species phylogenies using coalescence times among sequences. Syst Biol 2009, 58:468-477. 10.1093/sysbio/syp031, 20525601.
-
(2009)
Syst Biol
, vol.58
, pp. 468-477
-
-
Liu, L.1
Yu, L.2
Pearl, D.K.3
Edwards, S.V.4
-
6
-
-
84890563476
-
Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood
-
Wu Y. Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood. Evolution 2011,,
-
(2011)
Evolution
-
-
Wu, Y.1
-
7
-
-
43549090646
-
Rooted triple consensus and anomalous gene trees
-
10.1186/1471-2148-8-118, 2409437, 18439266
-
Ewing GB, Ebersberger I, Schmidt HA, von Haeseler A. Rooted triple consensus and anomalous gene trees. BMC Evol Biol 2008, 8:118. 10.1186/1471-2148-8-118, 2409437, 18439266.
-
(2008)
BMC Evol Biol
, vol.8
, pp. 118
-
-
Ewing, G.B.1
Ebersberger, I.2
Schmidt, H.A.3
von Haeseler, A.4
-
8
-
-
67449167484
-
Properties of consensus methods for inferring species trees from gene trees
-
10.1093/sysbio/syp008, 2909780, 20525567
-
Degnan JH, DeGiorgio M, Bryant D, Rosenberg NA. Properties of consensus methods for inferring species trees from gene trees. Syst Biol 2009, 58:35-54. 10.1093/sysbio/syp008, 2909780, 20525567.
-
(2009)
Syst Biol
, vol.58
, pp. 35-54
-
-
Degnan, J.H.1
DeGiorgio, M.2
Bryant, D.3
Rosenberg, N.A.4
-
9
-
-
79958164317
-
Performance of matrix representation with parsimony for inferring species from gene trees
-
Wang Y, Degnan JH. Performance of matrix representation with parsimony for inferring species from gene trees. Stat Appl Genet Mol Biol 2011, 10:21.
-
(2011)
Stat Appl Genet Mol Biol
, vol.10
, pp. 21
-
-
Wang, Y.1
Degnan, J.H.2
-
10
-
-
77249086587
-
Bayesian inference of species trees from multilocus data
-
10.1093/molbev/msp274, 2822290, 19906793
-
Heled J, Drummond AJ. Bayesian inference of species trees from multilocus data. Mol Biol Evol 2010, 27:570-580. 10.1093/molbev/msp274, 2822290, 19906793.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 570-580
-
-
Heled, J.1
Drummond, A.J.2
-
11
-
-
63549118031
-
STEM: Species tree estimation using maximum likelihood for gene trees under coalescence
-
10.1093/bioinformatics/btp079, 19211573
-
Kubatko LS, Carstens BC, Knowles LL. STEM: Species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 2009, 25:971-973. 10.1093/bioinformatics/btp079, 19211573.
-
(2009)
Bioinformatics
, vol.25
, pp. 971-973
-
-
Kubatko, L.S.1
Carstens, B.C.2
Knowles, L.L.3
-
12
-
-
34548575126
-
Species trees from gene trees: Reconstructing bayesian posterior distributions of a species phylogeny using estimated gene tree distributions
-
10.1080/10635150701429982, 17562474
-
Liu L, Pearl DK. Species trees from gene trees: Reconstructing bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst Biol 2007, 56:504-514. 10.1080/10635150701429982, 17562474.
-
(2007)
Syst Biol
, vol.56
, pp. 504-514
-
-
Liu, L.1
Pearl, D.K.2
-
13
-
-
80051975928
-
Estimating species trees from unrooted gene trees
-
10.1093/sysbio/syr027, 21447481
-
Liu L, Yu L. Estimating species trees from unrooted gene trees. Syst Biol 2011, 60:661-667. 10.1093/sysbio/syr027, 21447481.
-
(2011)
Syst Biol
, vol.60
, pp. 661-667
-
-
Liu, L.1
Yu, L.2
-
14
-
-
70350247510
-
Maximum tree: a consistent estimator of the species tree
-
10.1007/s00285-009-0260-0, 19283383
-
Liu L, Yu L, Pearl DK. Maximum tree: a consistent estimator of the species tree. J Math Biol 2010, 60:95-106. 10.1007/s00285-009-0260-0, 19283383.
-
(2010)
J Math Biol
, vol.60
, pp. 95-106
-
-
Liu, L.1
Yu, L.2
Pearl, D.K.3
-
15
-
-
76849102326
-
Incomplete lineage sorting: consistent phylogeny estimation from multiple loci
-
Mossel E, Roch S. Incomplete lineage sorting: consistent phylogeny estimation from multiple loci. IEEE/ACM Trans Comp Biol Bioinf 2010, 7:166-171.
-
(2010)
IEEE/ACM Trans Comp Biol Bioinf
, vol.7
, pp. 166-171
-
-
Mossel, E.1
Roch, S.2
-
16
-
-
77958059433
-
Sources of error for species-tree estimation: Impact of mutational and coalescent effects on accuracy and implications for choosing among different methods
-
Huang H, He Q, Kubatko LS, Knowles LL. Sources of error for species-tree estimation: Impact of mutational and coalescent effects on accuracy and implications for choosing among different methods. Syst Biol 2009, 59:573-583.
-
(2009)
Syst Biol
, vol.59
, pp. 573-583
-
-
Huang, H.1
He, Q.2
Kubatko, L.S.3
Knowles, L.L.4
-
17
-
-
68049099068
-
Coalescent methods for estimating phylogenetic trees
-
10.1016/j.ympev.2009.05.033, 19501178
-
Liu L, Yu L, Kubatko LS, Pearl DK, Edwards SV. Coalescent methods for estimating phylogenetic trees. Mol Phylogenet Evol 2009, 53:320-328. 10.1016/j.ympev.2009.05.033, 19501178.
-
(2009)
Mol Phylogenet Evol
, vol.53
, pp. 320-328
-
-
Liu, L.1
Yu, L.2
Kubatko, L.S.3
Pearl, D.K.4
Edwards, S.V.5
-
18
-
-
84857993608
-
The probability distribution of ranked gene trees on a species tree
-
10.1016/j.mbs.2011.10.006, 22075548
-
Degnan JH, Rosenberg N, Stadler T. The probability distribution of ranked gene trees on a species tree. Math Biosci 2012, 235:45-55. 10.1016/j.mbs.2011.10.006, 22075548.
-
(2012)
Math Biosci
, vol.235
, pp. 45-55
-
-
Degnan, J.H.1
Rosenberg, N.2
Stadler, T.3
-
19
-
-
13244292527
-
Gene tree distributions under the coalescent process
-
Degnan JH, Salter LA. Gene tree distributions under the coalescent process. Evolution 2005, 59:24-37.
-
(2005)
Evolution
, vol.59
, pp. 24-37
-
-
Degnan, J.H.1
Salter, L.A.2
-
20
-
-
34248368417
-
Counting coalescent histories
-
10.1089/cmb.2006.0109, 17563317
-
Rosenberg NA. Counting coalescent histories. J Comput Biol 2007, 14:360-377. 10.1089/cmb.2006.0109, 17563317.
-
(2007)
J Comput Biol
, vol.14
, pp. 360-377
-
-
Rosenberg, N.A.1
-
21
-
-
34250380386
-
Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions
-
10.1089/cmb.2007.A010, 17572027
-
Than C, Ruths D, Innan H, Nakhleh L. Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions. J Comput Biol 2007, 14:517-535. 10.1089/cmb.2007.A010, 17572027.
-
(2007)
J Comput Biol
, vol.14
, pp. 517-535
-
-
Than, C.1
Ruths, D.2
Innan, H.3
Nakhleh, L.4
-
22
-
-
0001650804
-
Estimation of the branch points of a branching diffusion process
-
Edwards AWF. Estimation of the branch points of a branching diffusion process. J R Stat Soc Ser B 1970, 32:155-174.
-
(1970)
J R Stat Soc Ser B
, vol.32
, pp. 155-174
-
-
Edwards, A.W.F.1
-
24
-
-
0021514720
-
Line-of-descent and genealogical processes, and their applications in population genetics models
-
10.1016/0040-5809(84)90027-3, 6505980
-
Tavaré S. Line-of-descent and genealogical processes, and their applications in population genetics models. Theor Popul Biol 1984, 26:119-164. 10.1016/0040-5809(84)90027-3, 6505980.
-
(1984)
Theor Popul Biol
, vol.26
, pp. 119-164
-
-
Tavaré, S.1
-
25
-
-
65649112683
-
-
Greenwood Village: Roberts & Company
-
Wakeley J. Coalescent Theory 2008, Greenwood Village: Roberts & Company.
-
(2008)
Coalescent Theory
-
-
Wakeley, J.1
-
26
-
-
0023822631
-
Relationships between gene trees and species trees
-
Pamilo P, Nei M. Relationships between gene trees and species trees. Mol Biol Evol 1988, 5:568-583.
-
(1988)
Mol Biol Evol
, vol.5
, pp. 568-583
-
-
Pamilo, P.1
Nei, M.2
-
27
-
-
0036515730
-
The probability of topological concordance of gene trees and species trees
-
Rosenberg NA. The probability of topological concordance of gene trees and species trees. Theor Pop Biol 2002, 61:225-247.
-
(2002)
Theor Pop Biol
, vol.61
, pp. 225-247
-
-
Rosenberg, N.A.1
-
29
-
-
0021426157
-
Fast algorithms for finding nearest common ancestors
-
Harel D, Tarjan RE. Fast algorithms for finding nearest common ancestors. SIAM J Comput 1984, 13:338-355.
-
(1984)
SIAM J Comput
, vol.13
, pp. 338-355
-
-
Harel, D.1
Tarjan, R.E.2
-
30
-
-
0024144496
-
On finding lowest common ancestors: simplification and parallelization
-
Schiever B, Vishkin U. On finding lowest common ancestors: simplification and parallelization. SIAM J Comput 1988, 17:1253-1262.
-
(1988)
SIAM J Comput
, vol.17
, pp. 1253-1262
-
-
Schiever, B.1
Vishkin, U.2
-
31
-
-
51349098340
-
Phylonet: A software package for analyzing and reconstructing reticulate evolutionary relationships
-
10.1186/1471-2105-9-322, 2533029, 18662388
-
Than C, Ruths D, Nakhleh L. Phylonet: A software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformatics 2008, 9:322. 10.1186/1471-2105-9-322, 2533029, 18662388.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 322
-
-
Than, C.1
Ruths, D.2
Nakhleh, L.3
-
32
-
-
38649110663
-
Beast: Bayesian evolutionary analysis by sampling trees
-
Drummond AJ, Rambaut A. Beast: Bayesian evolutionary analysis by sampling trees. BMC Evolut Biol 2007, 7:214.
-
(2007)
BMC Evolut Biol
, vol.7
, pp. 214
-
-
Drummond, A.J.1
Rambaut, A.2
-
33
-
-
79956154434
-
Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent
-
10.1007/s00285-010-0355-7, 20652704
-
Allman ES, Degnan JH, Rhodes JA. Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent. J Math Biol 2011, 62:833-862. 10.1007/s00285-010-0355-7, 20652704.
-
(2011)
J Math Biol
, vol.62
, pp. 833-862
-
-
Allman, E.S.1
Degnan, J.H.2
Rhodes, J.A.3
|