Next: Appendix
Up: Using Traveling Salesman Problem
Previous: Discussion
- 1
-
R. Agarwala, V. Bafna, M. Farach, B. Narangyan, M. Paterson, and M. Thorup.
On the approximability of numerical taxonomy: fitting distances with
trees.
SIAM J. Comput., pages 365 - 72, 1996.
- 2
-
Steven A. Benner, Mark A. Cohen, and Gaston H. Gonnet.
Empirical and structural models for insertions and deletions in the
divergent evolution of proteins.
J. Molecular Biology, 229:1065-1082, 1993.
- 3
-
Humberto Carillo and David. Lipman.
The multiple sequence alignment problem in biology.
SIAM J. Appl. Math., 48(5):1073-1082, 1988.
- 4
-
L. Cavalli-Sforza and A. Edwards.
Phylogenetic analysis: models and estimation procedures.
Evolution, 32:233 -57, 1967.
- 5
-
Margaret O. Dayhoff, R. M. Schwartz, and B. C. Orcutt.
A model for evolutionary change in proteins.
In Margaret O. Dayhoff, editor, Atlas of Protein Sequence and
Structure, volume 5, pages 345-352. 1978.
- 6
-
A. Dress and M. Steel.
Convex tree realization of partitions.
Appl. Math. Lett., 5:3 - 6, 1993.
- 7
-
G. Estabrook, C. Johnson, and F. McMorris.
An idealized concept of the true cladistic character.
Math. Biosciences, 23:263 - 72, 1975.
- 8
-
G. Estabrook, C. Johnson, and F. McMorris.
A mathematical foundation for the analysis of cladistic character
compatibility.
Math. Biosciences, 29:181 - 87, 1976.
- 9
-
J. Felsenstein.
Maximum-likelihood estimation of evolutionary trees from continuous
characters.
Amer. J. Human Genetics, 25:471-492, 1973.
- 10
-
J. Felsenstein.
The number of evolutionary trees.
Systematic Zoology, 27:401 - 410, 1978.
- 11
-
J. Felsenstein.
Evolutionary trees from gene frequencies and quantitative characters:
finding maximum likelihood estimates.
Evolution, 35:1229-1242, 1981.
- 12
-
W.M. Fitch and E. Margoliash.
The construction of phylogenetic trees.
Science, 155:279 - 84, 1967.
- 13
-
Gaston H. Gonnet and Steven A. Benner.
Probabilistic ancestral sequences and multiple alignments.
In Fifth Scandinavian Workshop on Algorithm Theory, Reykjevik
July 1996, 1996.
- 14
-
Gaston H. Gonnet, Mark A. Cohen, and Steven A. Benner.
Exhaustive matching of the entire protein sequence database.
Science, 256:1443-1445, 1992.
- 15
-
Gaston H. Gonnet and Chantal Korostensky.
Evaluation measures of multiple sequence alignments.
J. Comp. Biol., 1999.
submitted.
- 16
-
O. Gotoh.
An improved algorithm for matching biological sequences.
J. Mol. Biol., 162:705-708, 1982.
- 17
-
M. Groetschel and O. Holland.
Solution of large-scale symmetric traveling salesman problems.
Math. Programming, pages 141 - 202, 1991.
- 18
-
S. Gupta, J. Kececioglu, and A. Schaffer.
Making the shortest-paths approach to sum-of-pairs multiple sequence
alignment more space efficient in practice.
Proc. 6th Symp. on Combinatorial Pattern Matching, pages 128 -
43, 1995.
- 19
-
Sandeep K. Gupta, John Kececioglu, and Alejandro A. Schaffer.
Improving the practical space and time efficiency of the
shortest-paths approach to sum-of-pairs multiple sequence alignment.
In J. Computational Biology, 1996.
- 20
-
J. Hein.
An optimal algorithm to reconstruct trees from additive distance
data.
Bull. Math. Biol., 51:597 - 603, 1989.
- 21
-
P. Hogeweg and P. Hesper.
The alignmen of sets of sequences and the construction of
phylogenetic trees: an integrated method.
J. Mol. Evol., 20:175 -86, 1988.
- 22
-
T. Jiang and L. Wang.
On the complexity of multiple sequence alignment.
J. Comp. Biol., 1:337 - 48, 1994.
- 23
-
D.S. Johnson.
More approaches to the travelling salesman guide.
Nature, 330:525, December 1987.
- 24
-
D.S. Johnson.
Local optimization and the traveling salesman problem.
In Proc. 17th Colloq. on Automata, Languages and Programming,
volume 443 of Lecture Notes in Computer Science, pages 446 - 461,
Berlin, 1990. Springer Verlag.
- 25
-
J. Kececioglu.
The maximum weight trace problem in multiple sequence alignment.
Proc. 4th Symp. on Combinatorial Pattern Matching, pages 106 -
19, 1993.
- 26
-
Ch. Korostensky and G. Gonnet.
Gap heuristics and tree construction using gaps.
Technical Report, Inst. of Scientific Computing, ETH Zuerich,
321, 1999.
- 27
-
M. Padberg and G. Rinaldi.
A branch-and-cut algorithm for the resolution of large-scale
symmetric traveling salesman problems.
SIAM Review, 33:60 - 100, 1991.
- 28
-
D. Sankoff.
Minimal mutation trees of sequences.
SIAM J. Appl. Math., 28(35 - 42), 1975.
- 29
-
Temple F. Smith and Michael S. Waterman.
Identification of common molecular subsequences.
J. Mol. Biol., 147:195-197, 1981.
- 30
-
Jeffrey Thorne, Hirohisa Kishino, and Joseph Felsenstein.
Inching toward reality: An improved likelihood model of sequence
evolution.
J. Molecular Biology, 34:3-16, 1993.
Chantal Korostensky
1999-07-14