next up previous
Next: About this document ... Up: DeepForest ver.1.0 Manual Previous: How to get prototype

Bibliography

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