-
2
-
-
0000673494
-
Reconstructing the shape of a tree from observed dissimilarity data
-
Bandelt H.J., Dress A. 1986. Reconstructing the shape of a tree from observed dissimilarity data. Adv. Appl. Math. 7:309-343.
-
(1986)
Adv. Appl. Math.
, vol.7
, pp. 309-343
-
-
Bandelt, H.J.1
Dress, A.2
-
3
-
-
0002844544
-
Combining trees as a way of combining data sets for phylogenetic inference
-
Baum B.R. 1992. Combining trees as a way of combining data sets for phylogenetic inference. Taxon. 41:3-10.
-
(1992)
Taxon.
, vol.41
, pp. 3-10
-
-
Baum, B.R.1
-
4
-
-
0001117764
-
Inferring evolutionary trees with strong combinatorial evidence
-
Berry V., Gascuel O. 2001. Inferring evolutionary trees with strong combinatorial evidence. Theor. Comput. Sci. 240:271-298.
-
(2001)
Theor. Comput. Sci.
, vol.240
, pp. 271-298
-
-
Berry, V.1
Gascuel, O.2
-
5
-
-
0348142485
-
Constructing optimal trees from quartets
-
Bryant D., Steel M.A. 2001. Constructing optimal trees from quartets. J. Algorithms. 38:237-259.
-
(2001)
J. Algorithms.
, vol.38
, pp. 237-259
-
-
Bryant, D.1
Steel, M.A.2
-
6
-
-
0002074731
-
The recovery of trees from measures of dissimilarity
-
F.R. Hodson, Kendall D.G., Tautu P., editors Mamaia, Romania: Edinburgh University Press
-
Buneman P. 1971. The recovery of trees from measures of dissimilarity. In: F.R. Hodson, Kendall D.G., Tautu P., editors. Anglo-Romanian Conference on Mathematics in the Archaeological and Historical Sciences. Mamaia, Romania: Edinburgh University Press p. 387-395.
-
(1971)
Anglo-Romanian Conference on Mathematics in the Archaeological and Historical Sciences
, pp. 387-395
-
-
Buneman, P.1
-
7
-
-
84917697072
-
Quartet inference from SNP data under the coalescent model
-
Chifman J., Kubatko L. 2014. Quartet inference from SNP data under the coalescent model. Bioinformatics. doi:10.1093/bioinformatics/btu530.
-
(2014)
Bioinformatics.
-
-
Chifman, J.1
Kubatko, L.2
-
8
-
-
12444268422
-
Molecular clock fork phylogenies: Closed form analytic maximum likelihood solutions
-
Chor B., Snir S. 2004. Molecular clock fork phylogenies: Closed form analytic maximum likelihood solutions. Syst. Biol. 53:963-967.
-
(2004)
Syst. Biol.
, vol.53
, pp. 963-967
-
-
Chor, B.1
Snir, S.2
-
9
-
-
0033795444
-
Multiple maxima of likelihood in phylogenetic trees: An analytic approach
-
Earlier version appeared in RECOMB 2000
-
Chor B., Hendy M., Holland B., Penny D. 2000. Multiple maxima of likelihood in phylogenetic trees: An analytic approach. Mol. Biol. Evol. 17:1529-1541. Earlier version appeared in RECOMB 2000.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 1529-1541
-
-
Chor, B.1
Hendy, M.2
Holland, B.3
Penny, D.4
-
10
-
-
33744462065
-
Maximum likelihood molecular clock comb: Analytic solutions
-
Earlier version appeared in RECOMB 2003
-
Chor B., Khetan A., Snir S. 2006. Maximum likelihood molecular clock comb: Analytic solutions. Jour. Comput. Biol. Earlier version appeared in RECOMB 2003.
-
(2006)
Jour. Comput. Biol.
-
-
Chor, B.1
Khetan, A.2
Snir, S.3
-
11
-
-
79960608276
-
Phylogenies without branch bounds: Contracting the short, pruning the deep
-
Daskalakis C., Mossel E., Roch S. 2011. Phylogenies without branch bounds: Contracting the short, pruning the deep. SIAM J. Discrete Math. 25:872-893.
-
(2011)
SIAM J. Discrete Math.
, vol.25
, pp. 872-893
-
-
Daskalakis, C.1
Mossel, E.2
Roch, S.3
-
12
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
Doolittle W.F. 1999. Phylogenetic classification and the universal tree. Science. 284:2124-9.
-
(1999)
Science
, vol.284
, pp. 2124-2129
-
-
Doolittle, W.F.1
-
14
-
-
84959752542
-
Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units
-
Estabrook G.F. 1985. Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units. Syst. Biol. 34:193-200.
-
(1985)
Syst. Biol.
, vol.34
, pp. 193-200
-
-
Estabrook, G.F.1
-
15
-
-
0000122573
-
PHYLIP - Phylogenetic inference package, (version 3.2)
-
Felsenstein J. 1989. PHYLIP - phylogenetic inference package, (version 3.2). Cladistics 5:164-166.
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
17
-
-
58449096222
-
Fast and reliable reconstruction of phylogenetic trees with very short branches
-
SODA
-
Gronau I., Moran S., Snir S. 2008. Fast and reliable reconstruction of phylogenetic trees with very short branches. In: ACM-SIAM Symposium on Discrete Algorithms (SODA), p. 379-388.
-
(2008)
ACM-SIAM Symposium on Discrete Algorithms
, pp. 379-388
-
-
Gronau, I.1
Moran, S.2
Snir, S.3
-
18
-
-
84871833016
-
Low-parameter phylogenetic inference under the general markov model
-
Holland B.R., Jarvis P.D., Sumner J.G. 2013. Low-parameter phylogenetic inference under the general markov model. Syst. Biol. 62:78-92.
-
(2013)
Syst. Biol.
, vol.62
, pp. 78-92
-
-
Holland, B.R.1
Jarvis, P.D.2
Sumner, J.G.3
-
19
-
-
0035706064
-
A polynomial time approximation scheme for inferring evolutionary trees from quartet topologies and its application
-
Jiang T., Kearney P.E., Li M. 2000. A polynomial time approximation scheme for inferring evolutionary trees from quartet topologies and its application. SIAM J. Comput. 30:1942-1961.
-
(2000)
SIAM J. Comput.
, vol.30
, pp. 1942-1961
-
-
Jiang, T.1
Kearney, P.E.2
Li, M.3
-
20
-
-
33845886105
-
Inferring phylogenetic networks by the maximum parsimony criterion: A case study
-
Jin G., Nakhleh L., Snir S., Tuller T. 2007. Inferring phylogenetic networks by the maximum parsimony criterion: a case study. Mol. Biol. Evol. 24:324-337.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 324-337
-
-
Jin, G.1
Nakhleh, L.2
Snir, S.3
Tuller, T.4
-
21
-
-
0034780910
-
Horizontal gene transfer in prokaryotes: Quantification and classification
-
Koonin E.V., Makarova K.S., Aravind L. 2001. Horizontal gene transfer in prokaryotes: quantification and classification. Annu. Rev. Microbiol. 55:709-742.
-
(2001)
Annu. Rev. Microbiol.
, vol.55
, pp. 709-742
-
-
Koonin, E.V.1
Makarova, K.S.2
Aravind, L.3
-
22
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
Ochman H., Lawrence J.G., Groisman E.A. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature. 405:299-304.
-
(2000)
Nature.
, vol.405
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.G.2
Groisman, E.A.3
-
23
-
-
0027104018
-
Matrix representation in reconstructing phylogenetic-relationships among the eukaryotes
-
Ragan M.A. 1992. Matrix representation in reconstructing phylogenetic-relationships among the eukaryotes. Biosystems. 28:47-55.
-
(1992)
Biosystems.
, vol.28
, pp. 47-55
-
-
Ragan, M.A.1
-
24
-
-
0034983479
-
Quartet-based phylogenetic inference: Improvements and limits
-
Ranwez V., Gascuel O. 2001. Quartet-based phylogenetic inference: Improvements and limits. Mole. Biol. Evol. 18:1103-1116.
-
(2001)
Mole. Biol. Evol.
, vol.18
, pp. 1103-1116
-
-
Ranwez, V.1
Gascuel, O.2
-
25
-
-
0019424782
-
Comparison of phylogenetic trees
-
Robinson D.R., Foulds L.R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131-147.
-
(1981)
Math. Biosci.
, vol.53
, pp. 131-147
-
-
Robinson, D.R.1
Foulds, L.R.2
-
27
-
-
0037314098
-
r8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
-
abstract. Available at http://ginger.ucdavis.edu/r8s
-
Sanderson M.J. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics. 19:301-302. doi:10.1093/bioinformatics/19.2.301. URL http://bioinformatics.oxfordjournals.org/content/19/2/301. abstract. Available at http://ginger.ucdavis.edu/r8s/
-
(2003)
Bioinformatics.
, vol.19
, pp. 301-302
-
-
Sanderson, M.J.1
-
29
-
-
85006612984
-
Quartets maxcut: A divide and conquer quartets algorithm
-
Snir S., Rao S. 2010. Quartets maxcut: A divide and conquer quartets algorithm. Trans. Comput. Biol. Bioinform. 7:714-718.
-
(2010)
Trans. Comput. Biol. Bioinform.
, vol.7
, pp. 714-718
-
-
Snir, S.1
Rao, S.2
-
30
-
-
83655184666
-
Quartet maxcut: A fast algorithm for amalgamating quartet trees
-
Snir S., Rao S. 2012. Quartet maxcut: A fast algorithm for amalgamating quartet trees. Mole. Phylogenet. Evol. 62:1-8.
-
(2012)
Mole. Phylogenet. Evol.
, vol.62
, pp. 1-8
-
-
Snir, S.1
Rao, S.2
-
31
-
-
84871573483
-
Reconstructing approximate phylogenetic trees from quartet samples
-
Preliminary version appeared in SODA 2010
-
Snir S., Yuster R. 2012. Reconstructing approximate phylogenetic trees from quartet samples. SIAM J. Comput. 41:1466-1480. Preliminary version appeared in SODA 2010.
-
(2012)
SIAM J. Comput.
, vol.41
, pp. 1466-1480
-
-
Snir, S.1
Yuster, R.2
-
32
-
-
39449105691
-
Short quartet puzzling: A new quartet-based phylogeny reconstruction algorithm
-
Snir S., Warnow T., Rao S. 2008. Short quartet puzzling: A new quartet-based phylogeny reconstruction algorithm. J. Comput. Biol. 1:91-103.
-
(2008)
J. Comput. Biol.
, vol.1
, pp. 91-103
-
-
Snir, S.1
Warnow, T.2
Rao, S.3
-
33
-
-
52449147252
-
The complexity of reconstructing trees from qualitative characters and subtress
-
Steel M. 1992. The complexity of reconstructing trees from qualitative characters and subtress. J. Classif. 9:91-116.
-
(1992)
J. Classif.
, vol.9
, pp. 91-116
-
-
Steel, M.1
-
34
-
-
0029836454
-
Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies
-
Available from URL
-
Strimmer K., von Haeseler A. 1996. Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies. Mole. Biol. Evol. 13:964-969. Available from URL ftp://ftp.ebi.ac.uk/pub/software/unix/puzzle/.
-
(1996)
Mole. Biol. Evol.
, vol.13
, pp. 964-969
-
-
Strimmer, K.1
Von Haeseler, A.2
-
37
-
-
84857250162
-
Superfine: Fast and accurate supertree estimation
-
Swenson M.S., Suri R., Linder C.R., Warnow T. 2012. Superfine: fast and accurate supertree estimation. Syst. Biol. 61:214-227. doi:10.1093/sysbio/syr092.
-
(2012)
Syst. Biol.
, vol.61
, pp. 214-227
-
-
Swenson, M.S.1
Suri, R.2
Linder, C.R.3
Warnow, T.4
-
38
-
-
84936060775
-
-
Sinauer, Sunderland, Mass.
-
Swofford D.L. 1998. PAUP∗beta, Sinauer, Sunderland, Mass.
-
(1998)
PAUP∗beta
-
-
Swofford, D.L.1
-
39
-
-
0032835111
-
Distinct types of RRNA operons exist in the genome of the actinomycete thermomonospora chromogena and evidence for horizontal transfer of an entire RRNA operon
-
Yap W.H., Zhang Z., Wang Y. 1999. Distinct types of RRNA operons exist in the genome of the actinomycete thermomonospora chromogena and evidence for horizontal transfer of an entire RRNA operon. J. Bacteriol. 181:5201-5209.
-
(1999)
J. Bacteriol.
, vol.181
, pp. 5201-5209
-
-
Yap, W.H.1
Zhang, Z.2
Wang, Y.3
-
40
-
-
33748277982
-
Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events
-
Zhaxybayeva O., Gogarten J.P., Charlebois R.L., Doolittle W.F., Papke R.T. 2006. Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome. Res. 16:1099-1108.
-
(2006)
Genome. Res.
, vol.16
, pp. 1099-1108
-
-
Zhaxybayeva, O.1
Gogarten, J.P.2
Charlebois, R.L.3
Doolittle, W.F.4
Papke, R.T.5
|