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- Adachi and Hasegawa, 1996
-
Adachi, J. and Hasegawa, M. (1996).
Computer science monographs, No. 28 MOLPHY Version 2.3:
Programs for Molecular Phylogenetics Based on Maximum Likelihood.
Institute of statistical mathematics, Tokyo.
- Cavalli-Sforza and Edwards, 1967
-
Cavalli-Sforza, L. L. and Edwards, A. W. F. (1967).
Phylogenetic analysis: Models and estimation procedures.
Amer. J. Hum. Genet., 19:233.
- Chikayama, 1998
-
Chikayama, T. (1998).
KL1 tutorial.
AITEC, Japan.
- Chikayama et al., 1988
-
Chikayama, T., Sato, H., and Miyazaki, T. (1988).
Overview of the parallel inference machine operating system
(PIMOS).
In Proceedings of FGCS'88, pages 230-251, Tokyo, Japan.
- Felsenstein, 1981
-
Felsenstein, J. (1981).
Evolutionary trees from DNA sequences: a maximum likelihood
approach.
J. Mol. Evol., 17(6):368-376.
- Felsenstein, 1993
-
Felsenstein, J. (1993).
PHYLIP: phylogeny inference package, ver. 3.5c.
University of Washington, Seattle.
- Foulds et al., 1979
-
Foulds, L. R., Penny, D., and Hendy, M. D. (1979).
A graph theoretic approach to the development of minimal phylogenetic
trees.
J. Mol. Evol., 13(2):151-166.
- Geenlaw et al., 1995
-
Geenlaw, R., Hoover, H. J., and Ruzzo, W. L. (1995).
Limits to parallel computation.
Oxford University Press.
- Geist et al., 1998
-
Geist, A., Beguelin, A., Dongarra, J., Jiang, W., Manchek, R., and Sunderam, V.
(1998).
PVM: Parallel Virtual Machine: A Users' Guide and Tutorial
for Networked Parallel Computing.
The MIT Press.
- Ina, 1994
-
Ina, Y. (1994).
ODEN: a program package for molecular evolutionary analysis and
database search of DNA and amino acid sequences.
Comput. Appl. Biosci., 10(1):11-12.
- Kuhner and Felsenstein, 1994
-
Kuhner, M. and Felsenstein, J. (1994).
A simulation comparison of phylogeny algorithms under equal and
unequal evolutionary rates.
Mol. Biol. Evol., 11:459-468.
- Lamport, 1995
-
Lamport, L. (1995).
A document preparation system: LaTeX.
Addison-Wesley Publishing Company.
- O'Keefe, 1994
-
O'Keefe, R. A. (1994).
The craft of prolog.
The MIT Press.
- Olsen et al., 1994
-
Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R. (1994).
fastDNAmL: a tool for construction of phylogenetic trees of DNA
sequences using maximum likelihood.
Comput. Appl. Biosci., 10(1):41-48.
- OOta, 1996
-
OOta, S. (1996).
Application of parallel logic programming for reconstruction of
molecular phylogenetic trees using the maximum likelihood method.
Master's thesis, Graduate School of Information Science, Japan
Advanced Institute of Science and Technology.
- OOta et al., 1995
-
OOta, S., Saitou, N., and Kunifuji, S. (1995).
Application of a parallel logic programming for reconstruction of
molecular phylogenetic trees using the maximum likelihood method.
In T. Chikayama, H. N. and Tick, E., editors, ICLP'95 Workshop
on Parallel Logic Programming, pages 61-72, Hayama.
- Saitou, 1996
-
Saitou, N. (1996).
Reconstruction of gene trees.
In Doolittle, R. F., editor, Methods in enzymology; Computer
Methods for Macromolecular Sequence Analysis, volume 266, pages 427-449.
Academic Press.
- Saitou and Imanishi, 1989
-
Saitou, N. and Imanishi, T. (1989).
Relative efficiencies of the Fitch-Margoliash, maximum-parsimony,
maximum-likelihood, minimum-evolution, and neighbor-joining methods of
phylogenetic tree construction in obtaining the correct tree.
Mol. Biol. Evol., 6(5):514-525.
- Saitou and Nei, 1987
-
Saitou, N. and Nei, M. (1987).
The neighbor-joining method: a new method for reconstructing
phylogenetic trees.
Mol. Biol. Evol., 4(4):406-425.
- Sekita, 1998
-
Sekita, D. (1998).
Inside KLIC.
AITEC, Japan.
- Shasha et al., 1994
-
Shasha, D., Wang, J. T., Zhang, K., and Shih, F. Y. (1994).
Exact and approximate algorithms for unordered tree matching.
IEEE Transactions on systems, Man and Cybernetics,
24(4):668-678.
- Sterling and Shapiro, 1986
-
Sterling, L. and Shapiro, E. (1986).
The art of prolog.
The MIT Press.
- Tanenbaum, 1987
-
Tanenbaum, A. S. (1987).
Operating systems: design and implementation.
Prentice-Hall, Inc.
- Thompson et al., 1994
-
Thompson, J., Higgins, D., and Gibson, T. (1994).
CLUSTAL W: improving the sensitivity of progressive multiple
sequence alignment through sequence weighting, position-specific gap
penalties and weight matrix choice.
Nucleic Acids Res., 22:4673-4680.
- Tick, 1991
-
Tick, E. (1991).
Parallel Logic Programming.
MIT Press, Cambridge, Massachusetts.
- Ueda, 1985
-
Ueda, K. (1985).
Guarded horn clauses.
Technical report, ICOT.
- Ueda and Chikayama, 1990
-
Ueda, K. and Chikayama, T. (1990).
Design of the kernel language for the parallel inference machine.
The computer journal.
- Winston, 1993
-
Winston, P. E. (1993).
Artificial intelligence.
ADDSON-WESLEY PUBLISHING COMPANY, third edition.
- Zhang and Shasha, 1989
-
Zhang, K. and Shasha, D. (1989).
Simple fast algorithms for the editing distance between trees and
related problems.
SIAM J. Comput., 18(6):1245-1262.
Satoshi OOta
1999-03-06