-
1
-
-
0032256591
-
On the approximability of numerical taxonomy (fitting distances by tree metrics)
-
R. Argawala, V. Bafna, M. Farach, M. Paterson, and M. Thorup, On the approximability of numerical taxonomy (fitting distances by tree metrics), SLAM J Comput 28 (1999), 1073-1085.
-
(1999)
SLAM J Comput
, vol.28
, pp. 1073-1085
-
-
Argawala, R.1
Bafna, V.2
Farach, M.3
Paterson, M.4
Thorup, M.5
-
2
-
-
0001656793
-
The performance of the neighbor-joining methods of phylogenetic reconstruction
-
K. Atteson, The performance of the neighbor-joining methods of phylogenetic reconstruction, Algorithmica 25 (1999), 251-278.
-
(1999)
Algorithmica
, vol.25
, pp. 251-278
-
-
Atteson, K.1
-
3
-
-
0026911267
-
-
H. Bandelt and A. Dress, Split decomposition: A new and useful approach to phylogenetic analysis of distance data, MoI Phylogenet Evol 1 (1992), 242-252.
-
H. Bandelt and A. Dress, Split decomposition: A new and useful approach to phylogenetic analysis of distance data, MoI Phylogenet Evol 1 (1992), 242-252.
-
-
-
-
5
-
-
0015951616
-
A molecular sequence metric and evolutionary trees
-
W.A. Beyer, M. Stein, T. Smith, and S. Ulam, A molecular sequence metric and evolutionary trees, Math Biosci 19 (1974), 9-25.
-
(1974)
Math Biosci
, vol.19
, pp. 9-25
-
-
Beyer, W.A.1
Stein, M.2
Smith, T.3
Ulam, S.4
-
7
-
-
0033984609
-
Weighted neighbor-joining: A likelihood-based approach to distance-based phylogeny reconstruction
-
W.J. Bruno, M.D. Socci, and A.L. Halpern, Weighted neighbor-joining: A likelihood-based approach to distance-based phylogeny reconstruction, Mol Biol Evol 17 (2000), 189-197.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 189-197
-
-
Bruno, W.J.1
Socci, M.D.2
Halpern, A.L.3
-
8
-
-
0031716190
-
Rapid evaluation of least-squares and minimum evolution criteria on phylogenetic trees
-
D. Bryant and P. Waddell, Rapid evaluation of least-squares and minimum evolution criteria on phylogenetic trees, Mol Biol Evol 15 (1998), 1346-1359.
-
(1998)
Mol Biol Evol
, vol.15
, pp. 1346-1359
-
-
Bryant, D.1
Waddell, P.2
-
9
-
-
0026005922
-
Use of the method of generalized least-squares in reconstructing phylogenies from sequence data
-
M. Bulmer, Use of the method of generalized least-squares in reconstructing phylogenies from sequence data, Mol Biol Evol 8 (1991), 868-883.
-
(1991)
Mol Biol Evol
, vol.8
, pp. 868-883
-
-
Bulmer, M.1
-
10
-
-
0002074731
-
-
F.R. Hodson, D.G. Kendall, and P. Tautu Editors, Edinburgh University Press, Edinburgh, UK
-
P. Buneman, "The recovery of trees from measure of dissimilarities, Archaeological and historical science," F.R. Hodson, D.G. Kendall, and P. Tautu (Editors), Edinburgh University Press, Edinburgh, UK, 1971, pp. 387-395.
-
(1971)
The recovery of trees from measure of dissimilarities, Archaeological and historical science
, pp. 387-395
-
-
Buneman, P.1
-
11
-
-
33645105055
-
A non-linear optimization procedure to estimate distances and instantaneous substitution rate matrices under the GTR model
-
D. Catanzaro, R. Pesenti, and M. Milinkovitch, A non-linear optimization procedure to estimate distances and instantaneous substitution rate matrices under the GTR model, Bioinformatics 22 (2006), 708-715.
-
(2006)
Bioinformatics
, vol.22
, pp. 708-715
-
-
Catanzaro, D.1
Pesenti, R.2
Milinkovitch, M.3
-
12
-
-
0000075010
-
Analysis of human evolution
-
Pergamon Press, Oxford, UK
-
L.L. Cavalli-Sforza and A.W.F Edwards, Analysis of human evolution, Proc XI Int Congress Genet, Pergamon Press, Oxford, UK, 1963, pp. 923-933.
-
(1963)
Proc XI Int Congress Genet
, pp. 923-933
-
-
Cavalli-Sforza, L.L.1
Edwards, A.W.F.2
-
13
-
-
0014082615
-
Phylogenetic analysis: Models and estimation procedures
-
L.L. Cavalli-Sforza and A.W.F. Edwards, Phylogenetic analysis: Models and estimation procedures, Am J Hum Genet 19(1967), 233-257.
-
(1967)
Am J Hum Genet
, vol.19
, pp. 233-257
-
-
Cavalli-Sforza, L.L.1
Edwards, A.W.F.2
-
15
-
-
35048871573
-
An efficient exact algorithm for the minimum ultrametric tree problem
-
H.F. Chen and M.S. Chang, An efficient exact algorithm for the minimum ultrametric tree problem, Lecture Notes Comput Sci 3341 (2004), 282-293.
-
(2004)
Lecture Notes Comput Sci
, vol.3341
, pp. 282-293
-
-
Chen, H.F.1
Chang, M.S.2
-
16
-
-
35248869609
-
On the full and bottleneck full Steiner tree problems
-
Y.H. Chen, C.L.L. Lu, and C.Y. Tang, On the full and bottleneck full Steiner tree problems, Lecture Notes Comput Sei 2697 (2003), 122-129.
-
(2003)
Lecture Notes Comput Sei
, vol.2697
, pp. 122-129
-
-
Chen, Y.H.1
Lu, C.L.L.2
Tang, C.Y.3
-
17
-
-
29144484019
-
Maximum likelihood of evolutionary trees: Hardness and approximation
-
B. Chor and T. Tuller, Maximum likelihood of evolutionary trees: Hardness and approximation, Bioinformatics 21 (2005), i97-i106.
-
(2005)
Bioinformatics
, vol.21
-
-
Chor, B.1
Tuller, T.2
-
18
-
-
0036108575
-
Fast recovery of evolutionary trees with thousands of nodes
-
M. Csürös, Fast recovery of evolutionary trees with thousands of nodes, J Comput Biol 9 (2002), 277-297.
-
(2002)
J Comput Biol
, vol.9
, pp. 277-297
-
-
Csürös, M.1
-
19
-
-
0036214723
-
Provably fast and accurate recovery of evolutionary trees through harmonic greedy triplets
-
M. Csürös and Y. Kao, Provably fast and accurate recovery of evolutionary trees through harmonic greedy triplets, SIAM J Comput 31 (2001), 306-322.
-
(2001)
SIAM J Comput
, vol.31
, pp. 306-322
-
-
Csürös, M.1
Kao, Y.2
-
20
-
-
0024608695
-
A fast algorithm for constructing trees from distance matrices
-
J. Culberson and P. Rudnicki, A fast algorithm for constructing trees from distance matrices, Inform Process Lett 30 (1989), 215-220.
-
(1989)
Inform Process Lett
, vol.30
, pp. 215-220
-
-
Culberson, J.1
Rudnicki, P.2
-
21
-
-
33646192594
-
A multi-neighbor-joining approach for phylogenetic tree reconstruction and visualization
-
A.E. da Silva, W.J.P. Villanueva, H. Knidel, V. Bonato, S.F. dos Reis, and F.J.V. Zuben, A multi-neighbor-joining approach for phylogenetic tree reconstruction and visualization, Genet Mol Res 4 (2005), 525-534.
-
(2005)
Genet Mol Res
, vol.4
, pp. 525-534
-
-
da Silva, A.E.1
Villanueva, W.J.P.2
Knidel, H.3
Bonato, V.4
dos Reis, S.F.5
Zuben, F.J.V.6
-
22
-
-
0023079987
-
Computational complexity of inferring phylogenies from dissimilarity matrices
-
W.H.E. Day, Computational complexity of inferring phylogenies from dissimilarity matrices, B Math Biol 49 (1987), 461-467.
-
(1987)
B Math Biol
, vol.49
, pp. 461-467
-
-
Day, W.H.E.1
-
23
-
-
0037375006
-
On the consistency of the minimum evolution principle of phylogenetic inference
-
F. Denis and O. Gascuel, On the consistency of the minimum evolution principle of phylogenetic inference, Discrete Appl Math 127 (2003), 66-77.
-
(2003)
Discrete Appl Math
, vol.127
, pp. 66-77
-
-
Denis, F.1
Gascuel, O.2
-
24
-
-
0036943052
-
Fast and accurate phylogeny reconstruction algorithms based on the minimum evolution principle
-
R. Desper and O. Gascuel, Fast and accurate phylogeny reconstruction algorithms based on the minimum evolution principle, J Comput Biol 9 (2002), 687-705.
-
(2002)
J Comput Biol
, vol.9
, pp. 687-705
-
-
Desper, R.1
Gascuel, O.2
-
25
-
-
1542510099
-
Theoretical foundations of the balanced minimum evolution method of phylogenetic inference and its relationship to the weighted least-squares tree fitting
-
R. Desper and O. Gascuel, Theoretical foundations of the balanced minimum evolution method of phylogenetic inference and its relationship to the weighted least-squares tree fitting, Mol Biol Evol 21 (2004), 587-598.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 587-598
-
-
Desper, R.1
Gascuel, O.2
-
26
-
-
0002515505
-
Unrooted trees for numerical taxonomy
-
A.J. Dobson, Unrooted trees for numerical taxonomy, J Appl Probab 11 (1974), 32-42.
-
(1974)
J Appl Probab
, vol.11
, pp. 32-42
-
-
Dobson, A.J.1
-
27
-
-
0242487486
-
Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics
-
P. Erixon, B. Svennblad, T. Britton, and B. Oxelman, Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics, Syst Biol 52 (2003), 665-673.
-
(2003)
Syst Biol
, vol.52
, pp. 665-673
-
-
Erixon, P.1
Svennblad, B.2
Britton, T.3
Oxelman, B.4
-
28
-
-
0001192522
-
Distance methods and the approximation of most-parsimonious trees
-
D.P Faith, Distance methods and the approximation of most-parsimonious trees, Syst Zool 43 (1985), 312-325.
-
(1985)
Syst Zool
, vol.43
, pp. 312-325
-
-
Faith, D.P.1
-
29
-
-
0029192324
-
A robust model for finding optimal evolutionary trees
-
M. Farach, S. Kannan, and T. Warnow, A robust model for finding optimal evolutionary trees, Algorithmica 13 (1995), 155-179.
-
(1995)
Algorithmica
, vol.13
, pp. 155-179
-
-
Farach, M.1
Kannan, S.2
Warnow, T.3
-
30
-
-
84963036437
-
On the cophenetic correlation coefficient
-
J.S. Farris, On the cophenetic correlation coefficient, Syst Zool 18 (1969), 279-285.
-
(1969)
Syst Zool
, vol.18
, pp. 279-285
-
-
Farris, J.S.1
-
31
-
-
0000472542
-
Estimating phylogenetic trees from distance matrices
-
J.S. Farris, Estimating phylogenetic trees from distance matrices, Am Nat 106 (1972), 645-668.
-
(1972)
Am Nat
, vol.106
, pp. 645-668
-
-
Farris, J.S.1
-
32
-
-
84959798530
-
Cases in which parsimony or compatibility methods will be positively misleading
-
J. Felsenstein, Cases in which parsimony or compatibility methods will be positively misleading, Syst Zool 27 (1978), 401-410.
-
(1978)
Syst Zool
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
33
-
-
0019797407
-
A maximum likelihood approach
-
Evolutionary trees from DNA sequences
-
J. Felsenstein, Evolutionary trees from DNA sequences: A maximum likelihood approach, J MolI Evol 17 (1981), 368-376.
-
(1981)
J MolI Evol
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
34
-
-
0021581577
-
Distance methods for inferring phylogenies: A justification
-
J. Felsenstein, Distance methods for inferring phylogenies: A justification, Evolution 38 (1984), 16-24.
-
(1984)
Evolution
, vol.38
, pp. 16-24
-
-
Felsenstein, J.1
-
35
-
-
0031084471
-
An alternating least-squares approach to inferring phylogenies from pairwise distances
-
J. Felsenstein, An alternating least-squares approach to inferring phylogenies from pairwise distances, Syst Biol 46 (1997), 101-111.
-
(1997)
Syst Biol
, vol.46
, pp. 101-111
-
-
Felsenstein, J.1
-
37
-
-
0015162378
-
Rate of change of concomitantly variable codons
-
W.M. Fitch, Rate of change of concomitantly variable codons, J Mol Evol 1 (1971), 84-96.
-
(1971)
J Mol Evol
, vol.1
, pp. 84-96
-
-
Fitch, W.M.1
-
38
-
-
0014211361
-
Construction of phylogenetic trees
-
W.M. Fitch and E. Margoliash, Construction of phylogenetic trees, Sci 155 (1967), 279-284.
-
(1967)
Sci
, vol.155
, pp. 279-284
-
-
Fitch, W.M.1
Margoliash, E.2
-
39
-
-
0035029534
-
Maximum-likelihood phylogenetic analysis under covarion-like model
-
N. Galtier, Maximum-likelihood phylogenetic analysis under covarion-like model, Mol Biol Evol 18 (2001), 866-873.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 866-873
-
-
Galtier, N.1
-
41
-
-
0030807655
-
An improved version of the NJ algorithm based on a simple model of sequence data
-
BIONJ
-
O. Gascuel, BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data, Mol Biol Evol 14 (1997), 685-695.
-
(1997)
Mol Biol Evol
, vol.14
, pp. 685-695
-
-
Gascuel, O.1
-
42
-
-
0000194822
-
Concerning the NJ algorithm and its unweighted version
-
B. Mirkin, F.R. McMorris, F. Roberts, and A. Rzhetsky Editors, American Mathematical Society, Providence, RI
-
O. Gascuel, "Concerning the NJ algorithm and its unweighted version," UNJ, Mathematical hierarchies and biology, B. Mirkin, F.R. McMorris, F. Roberts, and A. Rzhetsky (Editors), American Mathematical Society, Providence, RI, 1997, pp. 149-170.
-
(1997)
UNJ, Mathematical hierarchies and biology
, pp. 149-170
-
-
Gascuel, O.1
-
43
-
-
63049111304
-
On the optimization principle in phylogenetic analysis and the minimum evolution criterion
-
O. Gascuel, On the optimization principle in phylogenetic analysis and the minimum evolution criterion, J Classif 19 (2000), 67-69.
-
(2000)
J Classif
, vol.19
, pp. 67-69
-
-
Gascuel, O.1
-
45
-
-
0035527361
-
Strengths and limitations of the minimum evolution principle
-
O. Gascuel, D. Bryant, and F. Denis, Strengths and limitations of the minimum evolution principle, Syst Biol 50 (2001), 621-627.
-
(2001)
Syst Biol
, vol.50
, pp. 621-627
-
-
Gascuel, O.1
Bryant, D.2
Denis, F.3
-
46
-
-
0030555957
-
A reduction algorithm for approximating a (non-metric) dissimilarity by a tree distance
-
O. Gascuel and D. Levy, A reduction algorithm for approximating a (non-metric) dissimilarity by a tree distance, J Classif 13 (1996), 129-155.
-
(1996)
J Classif
, vol.13
, pp. 129-155
-
-
Gascuel, O.1
Levy, D.2
-
47
-
-
3042528663
-
Performance analysis of hierarchical clustering algorithms
-
O. Gascuel and A. McKenzie, Performance analysis of hierarchical clustering algorithms, J Classif 21 (2004), 3-18.
-
(2004)
J Classif
, vol.21
, pp. 3-18
-
-
Gascuel, O.1
McKenzie, A.2
-
48
-
-
33749540417
-
Neighbor-joining revealed
-
O. Gascuel and M. Steel, Neighbor-joining revealed, Mol Biol Evol 23 (2006), 1997-2000.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1997-2000
-
-
Gascuel, O.1
Steel, M.2
-
49
-
-
0034120071
-
Evaluation measures of multiple sequence alignments
-
G.H. Gonnet, C. Korostensky, and S. Benner, Evaluation measures of multiple sequence alignments, J Comput Biol 7 (2000), 261-276.
-
(2000)
J Comput Biol
, vol.7
, pp. 261-276
-
-
Gonnet, G.H.1
Korostensky, C.2
Benner, S.3
-
50
-
-
0020308198
-
Unlikelihood that minimal phylogenies for a realistic biological study can be constructed in reasonable computational time
-
R.L. Graham and L.R. Foulds, Unlikelihood that minimal phylogenies for a realistic biological study can be constructed in reasonable computational time, Math Biosci 60 (1982), 133-142.
-
(1982)
Math Biosci
, vol.60
, pp. 133-142
-
-
Graham, R.L.1
Foulds, L.R.2
-
51
-
-
0029900516
-
A general additive distance with time-reversibility and rate variation among nucleotide sites
-
X. Gu and W.H. Li, A general additive distance with time-reversibility and rate variation among nucleotide sites, Proc Natl Acad Sci USA 93 (1996), 4671-4676.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 4671-4676
-
-
Gu, X.1
Li, W.H.2
-
52
-
-
0019797407
-
A maximum likelihood approach
-
Evolutionary trees from DNA sequences
-
M. Hasegawa, H. Kishino, and T. Yano, Evolutionary trees from DNA sequences: A maximum likelihood approach, J Mol Evol 17 (1981), 368-376.
-
(1981)
J Mol Evol
, vol.17
, pp. 368-376
-
-
Hasegawa, M.1
Kishino, H.2
Yano, T.3
-
53
-
-
0022376704
-
Dating the human-ape splitting by a molecular clock of mitochondrial DNA
-
M. Hasegawa. H. Kishino, and T. Yano, Dating the human-ape splitting by a molecular clock of mitochondrial DNA, J Mol Evol 22 (1985), 160-174.
-
(1985)
J Mol Evol
, vol.22
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
Yano, T.3
-
54
-
-
11944260381
-
Approaches for assessing phylogenetic accuracy
-
D.M. Hillis, Approaches for assessing phylogenetic accuracy, Syst Biol 44 (1995), 3-16.
-
(1995)
Syst Biol
, vol.44
, pp. 3-16
-
-
Hillis, D.M.1
-
56
-
-
11944268967
-
Performance of phylogenetic methods in simulation
-
J.P. Huelsenbeck, Performance of phylogenetic methods in simulation, Syst Biol 44 (1995), 17-48.
-
(1995)
Syst Biol
, vol.44
, pp. 17-48
-
-
Huelsenbeck, J.P.1
-
57
-
-
0036097894
-
Testing a covariotide model of DNA substitution
-
J.P. Huelsenbeck, Testing a covariotide model of DNA substitution, Mol Biol Evol 19 (2002), 698-707.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 698-707
-
-
Huelsenbeck, J.P.1
-
58
-
-
0035861456
-
Bayesian inference of phylogeny and its impact on evolutionary biology
-
J.P. Huelsenbeck, F. Ronquist, R. Nielsen, and J.P. Boll-back, Bayesian inference of phylogeny and its impact on evolutionary biology, Sci 294 (2001), 2310-2314.
-
(2001)
Sci
, vol.294
, pp. 2310-2314
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
Nielsen, R.3
Boll-back, J.P.4
-
59
-
-
0032746022
-
Disk-covering, a fast converging method for phylogenetic tree reconstruction
-
D. Huson, S. Nettles, and T. Warnow, Disk-covering, a fast converging method for phylogenetic tree reconstruction, J Comput Biol 6 (1999), 369-386.
-
(1999)
J Comput Biol
, vol.6
, pp. 369-386
-
-
Huson, D.1
Nettles, S.2
Warnow, T.3
-
60
-
-
0000732090
-
Evolution of protein molecules
-
H.N. Munro Editor, Academic Press, New York
-
T.H. Jukes and C. Cantor, "Evolution of protein molecules," Mammalian protein metabolism, H.N. Munro (Editor), Academic Press, New York, 1969, pp. 21-123.
-
(1969)
Mammalian protein metabolism
, pp. 21-123
-
-
Jukes, T.H.1
Cantor, C.2
-
61
-
-
0015059567
-
Phylogenetic analysis: Concepts and methods
-
K.K. Kidd and L.A. Sgaramella-Zonta, Phylogenetic analysis: Concepts and methods, Am J Hum Genet 23 (1971), 235-252.
-
(1971)
Am J Hum Genet
, vol.23
, pp. 235-252
-
-
Kidd, K.K.1
Sgaramella-Zonta, L.A.2
-
62
-
-
0019296687
-
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
-
M. Kimura, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, J Mol Evol 16(1980), 111-120.
-
(1980)
J Mol Evol
, vol.16
, pp. 111-120
-
-
Kimura, M.1
-
63
-
-
0038077526
-
On the complexity of distance-based evolutionary tree reconstruction
-
SIAM, Philadelphia, PA
-
V. King, L. Zhang, and Y. Zhou, On the complexity of distance-based evolutionary tree reconstruction, Proc Fourteenth Ann ACM-SIAM Symp Discr Algorithms, SIAM, Philadelphia, PA, 2003, pp. 444-453.
-
(2003)
Proc Fourteenth Ann ACM-SIAM Symp Discr Algorithms
, pp. 444-453
-
-
King, V.1
Zhang, L.2
Zhou, Y.3
-
64
-
-
0033759309
-
Using traveling salesman problem algorithms for evolutionary tree construction
-
C. Korostensky and G.H. Gonnet, Using traveling salesman problem algorithms for evolutionary tree construction, Bioinformatics 16 (2000), 619-627.
-
(2000)
Bioinformatics
, vol.16
, pp. 619-627
-
-
Korostensky, C.1
Gonnet, G.H.2
-
65
-
-
0028177080
-
A simulation comparison of phylogeny algorithms under equal and unequal rates
-
M.K. Kuhner and J. Felsenstein, A simulation comparison of phylogeny algorithms under equal and unequal rates, Mol Biol Evol 11 (1994), 584-593.
-
(1994)
Mol Biol Evol
, vol.11
, pp. 584-593
-
-
Kuhner, M.K.1
Felsenstein, J.2
-
66
-
-
0029917260
-
A stepwise algorithm for finding minimum evolution evolutionary trees
-
S. Kumar, A stepwise algorithm for finding minimum evolution evolutionary trees, Mol Biol Evol 13 (1996), 584-593.
-
(1996)
Mol Biol Evol
, vol.13
, pp. 584-593
-
-
Kumar, S.1
-
67
-
-
0021277009
-
A new method for calculating evolutionary substitution rates
-
C. Lanave, G. Preparata, C. Saccone, and G. Serio, A new method for calculating evolutionary substitution rates, J Mol Evol 20 (1984), 86-93.
-
(1984)
J Mol Evol
, vol.20
, pp. 86-93
-
-
Lanave, C.1
Preparata, G.2
Saccone, C.3
Serio, G.4
-
68
-
-
0032976397
-
Markov chain monte carlo algorithms for the Bayesian analysis of phylogenetic trees
-
B. Larget and D.L. Simon, Markov chain monte carlo algorithms for the Bayesian analysis of phylogenetic trees, Mol Biol Evol 16 (1999), 750-759.
-
(1999)
Mol Biol Evol
, vol.16
, pp. 750-759
-
-
Larget, B.1
Simon, D.L.2
-
69
-
-
11944272095
-
Statistical tests of DNA phylogenies
-
W.H. Li and A. Zharkikh, Statistical tests of DNA phylogenies, Syst Biol 44 (1995), 49-63.
-
(1995)
Syst Biol
, vol.44
, pp. 49-63
-
-
Li, W.H.1
Zharkikh, A.2
-
70
-
-
0036134757
-
Heterotachy : An important process of protein evolution
-
P. Lopez, D. Casane, and H. Philippe, Heterotachy : An important process of protein evolution, Mol Biol Evol 19 (2002), 1-7.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1-7
-
-
Lopez, P.1
Casane, D.2
Philippe, H.3
-
71
-
-
0042508856
-
The full Steiner tree problem
-
C.L. Lu, C.Y. Tang, and R.C.T. Lee, The full Steiner tree problem, Theor Comput Sci 306 (2003), 55-67.
-
(2003)
Theor Comput Sci
, vol.306
, pp. 55-67
-
-
Lu, C.L.1
Tang, C.Y.2
Lee, R.C.T.3
-
72
-
-
4544263561
-
A weighted least-squares approach for inferring phylogenies from incomplete distance matrices
-
V. Makarenkov and F.J. Lapointe, A weighted least-squares approach for inferring phylogenies from incomplete distance matrices, Bioinformatics 20 (2004), 2113-2121.
-
(2004)
Bioinformatics
, vol.20
, pp. 2113-2121
-
-
Makarenkov, V.1
Lapointe, F.J.2
-
73
-
-
0002651223
-
Circular orders of tree metrics and their uses for the reconstruction and fitting of phylogenetic trees
-
B. Mirkin, F.R. McMorris, F. Roberts, and A. Rzhetsky Editors, American Mathematical Society, Providence, RI
-
V. Makarenkov and B. Leclerc, "Circular orders of tree metrics and their uses for the reconstruction and fitting of phylogenetic trees," Mathematical hierarchies and biology, B. Mirkin, F.R. McMorris, F. Roberts, and A. Rzhetsky (Editors), American Mathematical Society, Providence, RI, 1997, pp. 183-208.
-
(1997)
Mathematical hierarchies and biology
, pp. 183-208
-
-
Makarenkov, V.1
Leclerc, B.2
-
74
-
-
0033243629
-
An algorithm for the fitting of a tree metric according to a weighted least-squares criterion
-
V. Makarenkov and B. Leclerc, An algorithm for the fitting of a tree metric according to a weighted least-squares criterion, J Classif 16 (1999), 3-26.
-
(1999)
J Classif
, vol.16
, pp. 3-26
-
-
Makarenkov, V.1
Leclerc, B.2
-
75
-
-
11944269526
-
Testing species phylogenies and phylogenetic methods with congruence
-
M.M. Mayamoto and W.M. Fitch, Testing species phylogenies and phylogenetic methods with congruence, Syst Biol 44 (1995), 64-76.
-
(1995)
Syst Biol
, vol.44
, pp. 64-76
-
-
Mayamoto, M.M.1
Fitch, W.M.2
-
79
-
-
0033928038
-
Direct calculation of a tree length using a distance matrix
-
Y. Pauplin, Direct calculation of a tree length using a distance matrix, J Mol Evol 51 (2000), 41-47.
-
(2000)
J Mol Evol
, vol.51
, pp. 41-47
-
-
Pauplin, Y.1
-
80
-
-
0033014993
-
Generalized neighbor-joining: More reliable phylogenetic tree reconstruction
-
W.R. Pearson, G. Robins, and T. Zhang, Generalized neighbor-joining: More reliable phylogenetic tree reconstruction, Mol Biol Evol 16 (1999), 806-816.
-
(1999)
Mol Biol Evol
, vol.16
, pp. 806-816
-
-
Pearson, W.R.1
Robins, G.2
Zhang, T.3
-
81
-
-
0007402667
-
Testing the theory of descendent
-
M.M. Mayamoto and J. Cracraft Editors, Oxford University Press, New York
-
D. Penny, M.D. Hendy, and M.A. Steel, "Testing the theory of descendent," Phylogenetic analysis of DNA sequences, M.M. Mayamoto and J. Cracraft (Editors), Oxford University Press, New York, 1991, pp. 155-183.
-
(1991)
Phylogenetic analysis of DNA sequences
, pp. 155-183
-
-
Penny, D.1
Hendy, M.D.2
Steel, M.A.3
-
82
-
-
33144459988
-
A short proof that phylogenetic tree reconstruction by maximum likelihood is hard, IEEE-ACM T
-
S. Roch, A short proof that phylogenetic tree reconstruction by maximum likelihood is hard, IEEE-ACM T Comput Biol 3 (2006), 92-94.
-
(2006)
Comput Biol
, vol.3
, pp. 92-94
-
-
Roch, S.1
-
83
-
-
0025267792
-
The general stochastic model of nucleotide substitution
-
F. Rodriguez, J.L. Oliver. A. Marin, and J.R. Medina, The general stochastic model of nucleotide substitution, J Theor Biol 142 (1990), 485-501.
-
(1990)
J Theor Biol
, vol.142
, pp. 485-501
-
-
Rodriguez, F.1
Oliver, J.L.2
Marin, A.3
Medina, J.R.4
-
84
-
-
0026466041
-
Statistical properties of the ordinary least-squares generalized least-squares and minimum evolution methods of phylogenetic inference
-
A. Rzhetsky and M. Nei, Statistical properties of the ordinary least-squares generalized least-squares and minimum evolution methods of phylogenetic inference, J Mol Evol 35 (1992), 367-375.
-
(1992)
J Mol Evol
, vol.35
, pp. 367-375
-
-
Rzhetsky, A.1
Nei, M.2
-
85
-
-
0027185401
-
Theoretical foundations of the minimum evolution method of phylogenetic inference
-
A. Rzhetsky and M. Nei, Theoretical foundations of the minimum evolution method of phylogenetic inference, Mol Biol Evol 10 (1993), 1073-1095.
-
(1993)
Mol Biol Evol
, vol.10
, pp. 1073-1095
-
-
Rzhetsky, A.1
Nei, M.2
-
86
-
-
0028129798
-
A program package for inferring and testing minimum evolution trees
-
METREE
-
A. Rzhetsky and M. Nei, METREE: A program package for inferring and testing minimum evolution trees, Comput Appl Biosci 10 (1994), 409-412.
-
(1994)
Comput Appl Biosci
, vol.10
, pp. 409-412
-
-
Rzhetsky, A.1
Nei, M.2
-
87
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
N. Saitou and M. Nei, The neighbor-joining method: A new method for reconstructing phylogenetic trees, Mol Biol Evol 4 (1987), 406-425.
-
(1987)
Mol Biol Evol
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
88
-
-
0000491446
-
Additive similarity trees
-
S. Sattah and A. Tversky, Additive similarity trees, Psychometrika 42 (1977), 319-345.
-
(1977)
Psychometrika
, vol.42
, pp. 319-345
-
-
Sattah, S.1
Tversky, A.2
-
90
-
-
2442636143
-
Cyclic permutations and evolutionary trees
-
C. Semple and M. Steel, Cyclic permutations and evolutionary trees, Adv Appl Math 32 (2004), 669-680.
-
(2004)
Adv Appl Math
, vol.32
, pp. 669-680
-
-
Semple, C.1
Steel, M.2
-
92
-
-
0024114801
-
A note on the neighbor-joining algorithm of Saitou and Nei
-
J.A. Studier and K.J. Keppler, A note on the neighbor-joining algorithm of Saitou and Nei, Mol Biol Evol 5 (1988), 729-731.
-
(1988)
Mol Biol Evol
, vol.5
, pp. 729-731
-
-
Studier, J.A.1
Keppler, K.J.2
-
93
-
-
63049138786
-
-
D.L. Swofford, PAUP* version 4.0, Sinauer, Sunderland, MA, 1997
-
D.L. Swofford, PAUP* version 4.0, Sinauer, Sunderland, MA, 1997.
-
-
-
-
94
-
-
0001336205
-
Phylogenetic inference
-
D.M. Hillis, C. Moritz, and B.K. Mable Editors, Sinauer & Associates, Sunderland, MA
-
D.L. Swofford, G.J. Olsen, P.J. Waddell, and D.M. Hillis, "Phylogenetic inference," Molecular systematics, D.M. Hillis, C. Moritz, and B.K. Mable (Editors), Sinauer & Associates, Sunderland, MA, 1996, pp. 407-514.
-
(1996)
Molecular systematics
, pp. 407-514
-
-
Swofford, D.L.1
Olsen, G.J.2
Waddell, P.J.3
Hillis, D.M.4
-
95
-
-
0020363837
-
Accuracy of estimated phylogenetic trees from molecular data
-
Y. Tateno, M. Nei, and F Tajima, Accuracy of estimated phylogenetic trees from molecular data, J Mol Evol 18 (1982), 387-404.
-
(1982)
J Mol Evol
, vol.18
, pp. 387-404
-
-
Tateno, Y.1
Nei, M.2
Tajima, F.3
-
96
-
-
0003364699
-
Least-squares approximation of additive trees
-
O. Opitz Editor, Springer-Verlag, Berlin
-
W. Vach, "Least-squares approximation of additive trees," Conceptual and numerical analysis of data, O. Opitz (Editor), Springer-Verlag, Berlin, 1989, pp. 230-238.
-
(1989)
Conceptual and numerical analysis of data
, pp. 230-238
-
-
Vach, W.1
-
97
-
-
0000948333
-
Least-squares approximation of additive trees to dissimilarities: Characterization and algorithms
-
W. Vach and P.O. Degens, Least-squares approximation of additive trees to dissimilarities: Characterization and algorithms, Comput Stat Q 3 (1991), 203-218.
-
(1991)
Comput Stat
, vol.Q 3
, pp. 203-218
-
-
Vach, W.1
Degens, P.O.2
-
98
-
-
0031297695
-
General time-reversible distances with unequal rates across sites: Mixing gamma and inverse gaussian distributions with invariant sites
-
P.J. Waddell and M.A. Steel, General time-reversible distances with unequal rates across sites: Mixing gamma and inverse gaussian distributions with invariant sites, Mol Phylogenet Evol 8 (1997), 398-414.
-
(1997)
Mol Phylogenet Evol
, vol.8
, pp. 398-414
-
-
Waddell, P.J.1
Steel, M.A.2
-
99
-
-
0017579898
-
Additive evolutionary trees
-
M.S. Waterman, T.F. Smith, M. Singh, and W.A. Beyer, Additive evolutionary trees, J Theor Biol 64 (1977), 199-213.
-
(1977)
J Theor Biol
, vol.64
, pp. 199-213
-
-
Waterman, M.S.1
Smith, T.F.2
Singh, M.3
Beyer, W.A.4
-
100
-
-
13744255040
-
Minimum evolution using ordinary least-squares is less robust than neighbor-joining
-
S.J. Willson, Minimum evolution using ordinary least-squares is less robust than neighbor-joining, B Math Biol 67 (2005), 261-279.
-
(2005)
B Math Biol
, vol.67
, pp. 261-279
-
-
Willson, S.J.1
-
101
-
-
0041542956
-
Approximation and exact algorithms for constructing minimum ultrametric trees from distance matrices
-
B.Y Wu, K.M. Chao, and C.Y. Tang, Approximation and exact algorithms for constructing minimum ultrametric trees from distance matrices, J Comb Optim 3 (1999), 199-211.
-
(1999)
J Comb Optim
, vol.3
, pp. 199-211
-
-
Wu, B.Y.1
Chao, K.M.2
Tang, C.Y.3
-
102
-
-
33847144208
-
Parallel branch-and-bound algorithm for constructing evolutionary trees from distance matrix
-
IEEE Computer Society
-
K.M. Yu, J. Zhou, C.Y Lin, and C.Y. Tang, Parallel branch-and-bound algorithm for constructing evolutionary trees from distance matrix, Proc 8th Inter Conf High-Perform Comput Asia-Pacific Region, IEEE Computer Society, 2005, pp. 66-72.
-
(2005)
Proc 8th Inter Conf High-Perform Comput Asia-Pacific Region
, pp. 66-72
-
-
Yu, K.M.1
Zhou, J.2
Lin, C.Y.3
Tang, C.Y.4
|