-
1
-
-
0002844544
-
Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees
-
Baum, B.R. 1992. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41, 3-10.
-
(1992)
Taxon
, vol.41
, pp. 3-10
-
-
Baum, B.R.1
-
2
-
-
1642519173
-
A classification of consensus methods for phylogenetics. DIMACS Series in discrete mathematics and theoretical computer science bioconsensus: DIMACS working group meetings on Bioconsensus, Oct. 25-26, 2003
-
Bryant, D. 1991. A Classification of Consensus Methods for Phylogenetics. DIMACS Series in Discrete Mathematics and Theoretical Computer Science. Bioconsensus: DIMACS working group meetings on Bioconsensus, Oct. 25-26, 2003, AMS, 61, 163-184.
-
(1991)
AMS
, vol.61
, pp. 163-184
-
-
Bryant, D.1
-
3
-
-
78549247493
-
IGTP: A software package for large-scale gene tree parsimony analysis
-
Chaudhary, R., Bansal, M.S. Wehe, A., et al. 2010. iGTP: a software package for large-scale gene tree parsimony analysis. BMC Bioinform, 11, 574.
-
(2010)
BMC Bioinform
, vol.11
, pp. 574
-
-
Chaudhary, R.1
Bansal, M.S.2
Wehe, A.3
-
4
-
-
79955380843
-
Comparing two Bayesian methods for gene tree/species tree reconstruction: A simulation with incomplete lineage sorting and horizontal gene transfer
-
Chung, Y., and Ané, C. 2011. Comparing two Bayesian methods for gene tree/species tree reconstruction: a simulation with incomplete lineage sorting and horizontal gene transfer. Syst. Biol. 60, 261-275.
-
(2011)
Syst. Biol
, vol.60
, pp. 261-275
-
-
Chung, Y.1
Ané, C.2
-
7
-
-
79960608276
-
Phylogenies without branch bounds: Contracting the short, pruning the deep
-
Daskalakis, C., Mossel, E., and Roch, S. 2011. Phylogenies without branch bounds: contracting the short, pruning the deep. SIAM J. Discr. Math 25, 872-893.
-
(2011)
SIAM J. Discr. Math
, vol.25
, pp. 872-893
-
-
Daskalakis, C.1
Mossel, E.2
Roch, S.3
-
8
-
-
65649131928
-
Gene tree discordance, phylogenetic inference and the multispecies coalescent
-
Degnan, J.H., and Rosenberg, N.A. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 26, 332-340.
-
(2009)
Trends Ecol. Evol
, vol.26
, pp. 332-340
-
-
Degnan, J.H.1
Rosenberg, N.A.2
-
9
-
-
67449167484
-
Properties of consensus methods for inferring species trees from gene trees
-
Degnan, J.H., DeGiorgio, M., Bryant, D., et al. 2009. Properties of consensus methods for inferring species trees from gene trees. Syst. Biol. 58, 35-54.
-
(2009)
Syst. Biol
, vol.58
, pp. 35-54
-
-
Degnan, J.H.1
Degiorgio, M.2
Bryant, D.3
-
10
-
-
58249100073
-
Is a new and general theory of molecular systematics emerging?
-
Edwards, S.V. 2009. Is a new and general theory of molecular systematics emerging? Evolution 63, 1-19.
-
(2009)
Evolution
, vol.63
, pp. 1-19
-
-
Edwards, S.V.1
-
11
-
-
0033480324
-
A few logs suffice to build (almost) all trees (i)
-
Erdos, P.L., Steel, M.A., Székely, L., et al. 1999a. A few logs suffice to build (almost) all trees (i). Random Struct. Algorithms 14 153-184.
-
(1999)
Random Struct. Algorithms
, vol.14
, pp. 153-184
-
-
Erdos, P.L.1
Steel, M.A.2
Székely, L.3
-
12
-
-
0001860411
-
A few logs suffice to build (almost) all trees (ii)
-
Erdos, P.L., Steel, M.A., Székely, L., et al. 1999b. A few logs suffice to build (almost) all trees (ii). Theor. Comput. Sci. 221, 77-118.
-
(1999)
Theor. Comput. Sci
, vol.221
, pp. 77-118
-
-
Erdos, P.L.1
Steel, M.A.2
Székely, L.3
-
13
-
-
84858438142
-
Fast and reliable reconstruction of phylogenetic trees with indistinguishable edges
-
Gronau, I., Moran, S., and Snir, S. 2011. Fast and reliable reconstruction of phylogenetic trees with indistinguishable edges. Random Struct. Algorithms. 40, 350-384.
-
(2011)
Random Struct. Algorithms
, vol.40
, pp. 350-384
-
-
Gronau, I.1
Moran, S.2
Snir, S.3
-
14
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of phyml 3.0
-
Guindon, S., Dufayard, J.F., Lefort, V., et al. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of phyml 3.0. Syst. Biol. 59 307-321.
-
(2010)
Syst. Biol
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.F.2
Lefort, V.3
-
15
-
-
77249086587
-
Bayesian inference of species trees from multilocus data
-
Heled, J., and Drummond, A.J. 2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27, 570-580.
-
(2010)
Mol. Biol. Evol
, vol.27
, pp. 570-580
-
-
Heled, J.1
Drummond, A.J.2
-
16
-
-
0032746022
-
Disk-covering, a fast converging method for phylogenetic tree reconstruction
-
Huson, D., Nettles, S., and Warnow T. 1999. Disk-covering, a fast converging method for phylogenetic tree reconstruction. J. Comput. Biol. 6, 369-386.
-
(1999)
J. Comput. Biol
, vol.6
, pp. 369-386
-
-
Huson, D.1
Nettles, S.2
Warnow, T.3
-
18
-
-
33644792802
-
Improvement in the acccuracy of multiple sequence alignment mafft
-
Katoh, K., Kuma, K., Miyata, T., et al. 2005a. Improvement in the acccuracy of multiple sequence alignment mafft. Genome Inform. 16 22-33.
-
(2005)
Genome Inform
, vol.16
, pp. 22-33
-
-
Katoh, K.1
Kuma, K.2
Miyata, T.3
-
19
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
Katoh, K., Kuma, K., Toh, H., et al. 2005b. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33, 511-518.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
-
20
-
-
78649687580
-
Accuracy of phylogeny reconstruction methods combining overlapping gene data sets
-
Kupczok, A., Schmidt, H., and von Haeseler, A. 2010. Accuracy of phylogeny reconstruction methods combining overlapping gene data sets. Algorithms Mol. Biol. 5, 37-53.
-
(2010)
Algorithms Mol. Biol
, vol.5
, pp. 37-53
-
-
Kupczok, A.1
Schmidt, H.2
Von Haeseler, A.3
-
21
-
-
78149256307
-
BUCKy: Gene tree/species tree reconciliation with the Bayesian concordance analysis
-
Larget, B., Kotha, S.K., Dewey, C.N., et al. 2010. BUCKy: Gene tree/species tree reconciliation with the Bayesian concordance analysis. Bioinformatics 26, 2910-2911.
-
(2010)
Bioinformatics
, vol.26
, pp. 2910-2911
-
-
Larget, B.1
Kotha, S.K.2
Dewey, C.N.3
-
22
-
-
64649099374
-
Phylogeny estimation and alignment via POY verss Clustal + PAUP*: A response to Ogden and Rosenberg
-
Lehtonen, S. 2008. Phylogeny estimation and alignment via POY verss Clustal + PAUP*: a response to Ogden and Rosenberg. Syst. Biol. 57, 653-657.
-
(2008)
Syst. Biol
, vol.57
, pp. 653-657
-
-
Lehtonen, S.1
-
23
-
-
84858612979
-
Treelength optimization for phylogeny estimation
-
Liu K., and Warnow, T. 2012. Treelength optimization for phylogeny estimation. PLoS ONE 7, e33104.
-
(2012)
PLoS ONE
, vol.7
-
-
Liu, K.1
Warnow, T.2
-
24
-
-
59649130312
-
Barking up the wrong treelength: The impact of gap penalty on alignment and tree accuracy
-
Liu, K., Nelesen, S., Raghavan, S., et al. 2009a. Barking up the wrong treelength: the impact of gap penalty on alignment and tree accuracy. IEEE Trans. Comput. Biol. Bioinform. 6, 7-21.
-
(2009)
IEEE Trans. Comput. Biol. Bioinform
, vol.6
, pp. 7-21
-
-
Liu, K.1
Nelesen, S.2
Raghavan, S.3
-
25
-
-
67649240664
-
Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees
-
Liu, K., Raghavan, S., Nelesen, S., et al. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science 324, 1561-1564.
-
(2009)
Science
, vol.324
, pp. 1561-1564
-
-
Liu, K.1
Raghavan, S.2
Nelesen, S.3
-
26
-
-
80053194704
-
Multiple sequence alignment: A major challenge to large-scale phylogenetics
-
Accessed April,1, 2012
-
Liu, K., Linder, C.R., and Warnow, T. 2010. Multiple sequence alignment: a major challenge to large-scale phylogenetics. PLoS Curr. Tree of Life Available at:http://knol.google.com/k/kevin-liu/multiple-sequence-alignment- amajor/ectabesw3uba/9. Accessed April 1, 2012.
-
(2010)
PLoS Curr. Tree of Life
-
-
Liu, K.1
Linder, C.R.2
Warnow, T.3
-
27
-
-
81455140612
-
RAxML and FastTree: Comparing two methods for large-scale maximum likelihood phylogeny estimation
-
Liu, K., Linder, C.R., and Warnow, T. 2011a. RAxML and FastTree: comparing two methods for large-scale maximum likelihood phylogeny estimation. PLoS ONE 6, e27731.
-
(2011)
PLoS ONE
, vol.6
-
-
Liu, K.1
Linder, C.R.2
Warnow, T.3
-
28
-
-
84555194934
-
SATé-II: Very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees
-
Liu, K., Warnow, T.J. Holder, M.T. et al. 2011b. SATé-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Syst. Biol. 61, 90-106.
-
(2011)
Syst. Biol
, vol.61
, pp. 90-106
-
-
Liu, K.1
Warnow, T.J.2
Holder, M.T.3
-
29
-
-
23044471766
-
An algorithm for progressive multiple alignment of sequences with insertions
-
Loytynoja A., and Goldman, N. 2005. An algorithm for progressive multiple alignment of sequences with insertions. Proc. Nat. Acad. Sci. 102, 10557-10562.
-
(2005)
Proc. Nat. Acad. Sci
, vol.102
, pp. 10557-10562
-
-
Loytynoja, A.1
Goldman, N.2
-
30
-
-
67649217482
-
Uniting alignments and trees
-
Loytynoja A., and Goldman, N. 2009. Uniting alignments and trees. Science 324, 1528-1529.
-
(2009)
Science
, vol.324
, pp. 1528-1529
-
-
Loytynoja, A.1
Goldman, N.2
-
31
-
-
27844472989
-
Statistical alignment: Recent progress, new applications, and challenges, 375-406
-
In Nielsen, R., ed (Statistics for Biology and Health) Springer, Berlin
-
Lunter, G., Drummond, A.J. Mikló s, I. et al. 2005. Statistical alignment: recent progress, new applications, and challenges, 375-406, In Nielsen, R., ed. Statistical Methods in Molecular Evolution (Statistics for Biology and Health). Springer, Berlin.
-
(2005)
Statistical Methods in Molecular Evolution
-
-
Lunter, G.1
Drummond, A.J.2
Miklós, I.3
-
32
-
-
0031504952
-
Gene trees in species trees
-
Maddison, W.P. 1997. Gene trees in species trees. Syst. Biol. 46, 523-536.
-
(1997)
Syst. Biol
, vol.46
, pp. 523-536
-
-
Maddison, W.P.1
-
33
-
-
77949341703
-
Toward extracting all phylogenetic information from matrices of evolutionary distances
-
Mossel, E. 2010. Toward extracting all phylogenetic information from matrices of evolutionary distances. Science 327, 1376-1379.
-
(2010)
Science
, vol.327
, pp. 1376-1379
-
-
Mossel, E.1
-
34
-
-
0035229987
-
Designing fast converging phylogenetic methods
-
Nakhleh, L., Roshan, U., St. John, K., et al. 2001a. Designing fast converging phylogenetic methods. Bioinformatics 17, 190-198.
-
(2001)
Bioinformatics
, vol.17
, pp. 190-198
-
-
Nakhleh, L.1
Roshan, U.2
St. John, K.3
-
35
-
-
84862587142
-
The performance of phylogenetic methods on trees of bounded diameter. 2149
-
Nakhleh, L., Roshan, U., St. John, K., et al. 2001b. The performance of phylogenetic methods on trees of bounded diameter. 2149, Lect. Notes Comput. Sci., 189-203.
-
(2001)
Lect. Notes Comput. Sci.
, pp. 189-203
-
-
Nakhleh, L.1
Roshan, U.2
St. John, K.3
-
39
-
-
34447277667
-
Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP*
-
Ogden, T.H., and Rosenberg, M. 2007. Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP*. Syst. Biol. 56, 182-193.
-
(2007)
Syst. Biol
, vol.56
, pp. 182-193
-
-
Ogden, T.H.1
Rosenberg, M.2
-
40
-
-
0042014724
-
The asymmetric median tree: A new model for building consensus trees
-
Phillips C.A., and Warnow, T. 1996. The asymmetric median tree: a new model for building consensus trees. Discr. Appl. Math. 71, 311-335.
-
(1996)
Discr. Appl. Math
, vol.71
, pp. 311-335
-
-
Phillips, C.A.1
Warnow, T.2
-
41
-
-
77949718257
-
FastTree 2-approximately maximum-likelihood trees for large alignments
-
Price, M.N., Dehal, P.S., and Arkin, A.P. 2010. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490.
-
(2010)
PLoS ONE
, vol.5
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
42
-
-
0026822436
-
Phylogenetic inference based on matrix representation of trees
-
Ragan, M.A. 1992. Phylogenetic inference based on matrix representation of trees. Mol. Phylogenet. Evol. 1, 53-58.
-
(1992)
Mol. Phylogenet. Evol
, vol.1
, pp. 53-58
-
-
Ragan, M.A.1
-
43
-
-
22844450838
-
Joint Bayesian estimation of alignment and phylogeny
-
Redelings, B., and Suchard, M. 2005. Joint Bayesian estimation of alignment and phylogeny. Syst. Biol. 54, 401-418.
-
(2005)
Syst. Biol
, vol.54
, pp. 401-418
-
-
Redelings, B.1
Suchard, M.2
-
44
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
Ronquist, F., and Huelsenbeck, J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
45
-
-
33750403801
-
RAxML-NI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis, A. 2006. RAxML-NI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
46
-
-
0011469880
-
Inverting random functions
-
Steel, M.A., and Székely, L.A. 1999. Inverting random functions. Ann. Comb. 3, 103-113.
-
(1999)
Ann. Comb
, vol.3
, pp. 103-113
-
-
Steel, M.A.1
Székely, L.A.2
-
47
-
-
0036662360
-
Inverting random functions. II. Explicit bounds for discrete maximum likelihood estimation, with applications
-
Steel, M.A., and Székely, L.A. 2002. Inverting random functions. II. Explicit bounds for discrete maximum likelihood estimation, with applications. SIAM J. Discr. Math. 15, 562-575.
-
(2002)
SIAM J. Discr. Math
, vol.15
, pp. 562-575
-
-
Steel, M.A.1
Székely, L.A.2
-
48
-
-
77949903642
-
A simulation study comparing supertree and combined analysis methods using SMIDGen
-
Swenson, M.S., Barbançon, F. Linder, C.R. et al. 2010. A simulation study comparing supertree and combined analysis methods using SMIDGen. Algorithms Mol. Biol. 5, 8.
-
(2010)
Algorithms Mol. Biol
, vol.5
, pp. 8
-
-
Swenson, M.S.1
Barbançon Linder, F.C.R.2
-
49
-
-
84858745309
-
SuperFine: Fast and accurate supertree estimation
-
abstract Accessed April 1 2012
-
Swenson, M.S., Suri, R., Linder, C.R. et al. 2011a. SuperFine: fast and accurate supertree estimation. Syst. Biol. Available at; http://sysbio. oxfordjournals.org/content/early/2011/09/16/sysbio.syr092.abstract. Accessed April 1, 2012.
-
(2011)
Syst. Biol.
-
-
Swenson, M.S.1
Suri, R.2
Linder, C.R.3
-
50
-
-
79955102024
-
An experimental study of Quartets MaxCut and other supertree methods
-
Swenson, M.S., Suri, R., Linder, C.R. et al. 2011b. An experimental study of Quartets MaxCut and other supertree methods. Algorithms Mol. Biol. 6, 7.
-
(2011)
Algorithms Mol. Biol
, vol.6
, pp. 7
-
-
Swenson, M.S.1
Suri, R.2
Linder, C.R.3
-
52
-
-
70349658769
-
Species tree inference by minimizing deep coalescences
-
Than, C.V., and Nakhleh, L. 2009. Species tree inference by minimizing deep coalescences. PLoS Comput. Biol. 5, e1000501.
-
(2009)
PLoS Comput. Biol
, vol.5
-
-
Than, C.V.1
Nakhleh, L.2
-
53
-
-
78651298101
-
Consistency properties of species tree inference by minimizing deep coalescences
-
Than, C.V., and Rosenberg, N.A. 2011. Consistency properties of species tree inference by minimizing deep coalescences. J. Comput Biol. 18, 1-15.
-
(2011)
J. Comput Biol
, vol.18
, pp. 1-15
-
-
Than, C.V.1
Rosenberg, N.A.2
-
54
-
-
51349098340
-
PhyloNet: A software package for analyzing and reconstructing reticulate evolutionary relationships
-
Than, C.V., Ruths, D., and Nakhleh, L. 2008. PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinform. 9, 322.
-
(2008)
BMC Bioinform
, vol.9
, pp. 322
-
-
Than, C.V.1
Ruths, D.2
Nakhleh, L.3
-
55
-
-
84862587138
-
POY software
-
Accessed April,1,2012
-
Varón, A., Vinh, L.S., Bomash, I., et al. 2007. POY software. Documentation. Available at: http://research.amnh.org/scicomp/projects/poy.php. Accessed April 1, 2012.
-
(2007)
Documentation
-
-
Varón, A.1
Vinh, L.S.2
Bomash, I.3
-
59
-
-
80053547401
-
Fast and accurate methods for phylogenomic analyses
-
Yang, J., and Warnow, T. 2011. Fast and accurate methods for phylogenomic analyses. BMC Bioinform. 12.
-
(2011)
BMC Bioinform.
, pp. 12
-
-
Yang, J.1
Warnow, T.2
-
60
-
-
80955136714
-
Algorithms for MDC-based multi-locus phylogeny inference: Beyond rooted binary gene trees on single alleles
-
Yu, Y., Warnow, T., and Nakhleh, L. 2011. Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles. J. Comput. Biol. 18, 1543-1559.
-
(2011)
J. Comput. Biol
, vol.18
, pp. 1543-1559
-
-
Yu, Y.1
Warnow, T.2
Nakhleh, L.3
|