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- Ajioka, J. W., Smoller, R. W., Jones, R. W., Carulli, J. P., Vellek, A. E. C., Garza, D., Link, A. K., Duncan, I. W., and Hartl, D. L. (1991).
- Drosophila genome project: one-hit coverage in yeast artificial chromosomes.
Chromosoma, 100:495-509.
- Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K., and Watson, J. D. (1994).
- Molecular Biology of the Cell.
Garland Publishing, New York, 3 edition.
- ANSI (1989).
- American national standard programming language C.
Technical Report X3.159-1989, American National Standard Institute.
- Ansorge, W., Voss, H., Wiemann, S., Schwager, C., Sproat, B., Zimmermann, J., Stegemann, J., Erfle, H., Hewitt, N., and Rupp, T. (1992).
- High-throughput automated DNA sequencing facility with fluorescent labels at the European Molecular Biology Laboratory.
Electrophoresis, 13:616-619.
- Ansorge, W., Zimmermann, J., Erfle, H., Hewitt, N., Rupp, T., Schwager, C., Sproat, B., Stegemann, J., and Voss, H. (1993).
- Sequencing reactions for ALF (EMBL) automated DNA sequencer.
Methods Mol. Biol., 23:317-356.
- Benson, D. A., Boguski, M., Lipman, D. J., and Ostell, J. (1994).
- GenBank.
Nucleic Acids Res., 22:3441-3444.
- Bhattacharya, D. (1996).
- Analysis of the distribution of bootstrap tree lengths using the maximum parsimony method.
Mol. Phyl. Evol., in Press.
- Bhattacharya, D., Damberger, S., Surek, B., and Melkonian, M. (1996).
- Primary and secondary structure analyses of the rRNA group-I introns of the zygnematales (charophyta).
Curr. Genet., 29:282-286.
- Bhattacharya, D. and Ehlting, J. (1995).
- Actin coding regions: Gene family evolution and use as a phylogenetic marker.
Arch. Protistenkd., 145:155-164.
- Bhattacharya, D., Helmchen, T., Bibeau, C., and Melkonian, M. (1995).
- Comparisons of nuclear-encoded small-subunit ribosomal RNAs reveal the evolutionary position of the Glaucocystophyta.
Mol. Biol. Evol., 12:415-420.
- Bhattacharya, D. and Medlin, L. (1995).
- The phylogeny of plastids: A review based on comparisons of small subunit ribosomal rna coding regions.
J. Phycol., 31:489-498.
- Bhattacharya, D., Stickel, S. K., and Sogin, M. L. (1993).
- Isolation and molecular phylogenetic analysis of actin-coding region from Emiliania huxleyi, a prymnesiophyte alga by reverse transcriptase and PCR-methods.
Mol. Biol. Evol., 10:689-703.
- Brandstädt, A. (1994).
- Graphen und Algorithmen.
B. G. Teubner, Stuttgart.
- Brown, J. K. (1994).
- Bootstrap hypothesis tests for evolutionary trees and other dendrograms.
Proc. Natl. Acad. Sci. USA, 91:12293-12297.
- Burkhardt, S. (1993).
- Parallele Rechnersysteme: Programmierung und Anwendung.
Verlag Technik, Berlin.
- Cavalli-Sforza, L. L. and Edwards, A. W. F. (1967).
- Phylogenetic analysis: Models and estimation procedures.
Amer. J. Human. Genet., 19:233-257.
- Cormen, T. H., Leiserson, C. E., and Rivest, R. (1990).
- Introduction to Algorithms.
MIT Press, Cambridge, Massachusetts.
- Curry, D. (1989).
- Using C on the UNIX System.
O'Reilly and Associates, Sebastopol.
- de Bellis, G., Consani, I., Caramenti, G., Pergallozzi, R., Debernardi, S., Invernizzi, L., and Luzzana, M. (1994).
- Mixed-mode fluorescent DNA sequencing.
Biotechniques, 16:1112-1115.
- Douglas, S. E. and Turner, S. (1991).
- Molecular evidence for the origin of plastids from a cyanobacterium-like ancestor.
J. Mol. Evol., 33:267-273.
- Efron, B. (1979).
- Bootstrap methods: Another look at the jackknife.
The Annals of Statistics, 7:1-26.
- Emmert, D. B., Stoehr, P. J., Stoesser, G., and Cameron, G. N. (1994).
- The European Bioinformatics Institute (EBI) databases.
Nucleic Acids Res., 22:3445-3449.
- Felsenstein, J. (1978).
- The number of evolutionary trees.
Syst. Zool., 27:27-33.
- Felsenstein, J. (1981).
- Evolutionary trees from DNA sequences: a maximum likelihood approach.
J. Mol. Evol., 17:368-376.
- Felsenstein, J. (1982).
- Numerical methods for inferring evolutionary trees.
The Quarterly Review of Biology, 57:379-404.
- Felsenstein, J. (1985).
- Confidence limits on phylogenies: an approach using the bootstrap.
Evolution, 39:783-791.
- Felsenstein, J. (1988).
- Phylogenies from molecular sequences: Inference and reliability.
Annu. Rev. Genet., 22:521-565.
- Felsenstein, J. (1990).
- PHYLIP manual, version 3.3.
University of Washington, Seattle.
- Felsenstein, J. (1993).
- PHYLIP manual, version 3.5.
University of Washington, Seattle.
- Fisher, R. A. (1912).
- The maximum-likelihood-method.
Messenger in Mathematics, 41:155-160.
- Fitch, W. M. and Margoliash, E. (1967).
- Construction of phylogenetic trees.
Science, 155:279-284.
- Frisch, Æ. (1991).
- Essential System Administration.
O'Reilly and Associates, Sebastopol.
- Futuyma, D. J. (1986).
- Evolutionary Biology.
Sinnauer Associates, Sunderland, Massachusetts.
- Gilly, D. (1992).
- UNIX in a Nutshell.
O'Reilly and Associates, Sebastopol.
- Goffeau, A. and Vassarotti, A. (1991).
- The european project for sequencing the yeast genome.
Res. Microbiol., 142.
- Goldman, N. (1990).
- Maximum likelihood inference of phylogenetic trees, with special reference to a poisson process model of DNA substitution and to parsimony analyses.
Syst. Zool., 39:345-361.
- Gropp, W., Lusk, E., and Skjellum, A. (1994).
- Using MPI.
MIT Press, Cambridge, Massachusetts.
- Haeckel, E. (1866).
- Generelle Morphologie der Organismen: Allgemeine Grundzüge der organischen Formen-Wissenschaft mechanisch begründet durch die von Charles Darvin reformierte Descendenz-Theorie.
Georg Riemer, Berlin.
- Harbison, S. P. and Steele Jr., G. L. (1991).
- C - A Reference Manual.
Prentice Hall, Englewood Cliffs, 3 edition.
- Hasegawa, M., Kishino, H., and Yano, T.-A. (1985).
- Dating of the human-ape splitting by a molecular clock of mitochondrial DNA.
J. Mol. Evol., 22:160-174.
- Hedges, S. B. (1992).
- The number of replications needed for accurate estimation of the bootstrap P value in phylogenetic studies.
Mol. Biol. Evol., 9:366-369.
- Helmchen, T. A., Bhattacharya, D., and Melkonian, M. (1995).
- Analyses of ribosomal RNA sequences from glaucocystophyte cyanelles provide new insights into the evolutionary relationship of plastids.
J. Mol. Evol., 41:203-210.
- Hillis, D. M. and Bull, J. J. (1993).
- An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analyses.
Syst. Biol., 42:182-192.
- Jukes, T. H. and Cantor, C. R. (1969).
- Evolution of protein molecules.
In Munro, H. N., editor, Mammalian Protein Metabolism. Academic Press, New York.
- Jülich, A. (1995).
- Implementations of BLAST for parallel computers.
CABIOS, 11:3-6.
- Keller, U. (1995).
- Pallas GmbH, Brühl.
Personal communication.
- Kerninghan, B. W. and Ritchie, D. M. (1988).
- The C Programming Language.
Prentice Hall, Englewood Cliffs, 2 edition.
- Kimura, M. (1980).
- A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
J. Mol. Evol., 16:111-120.
- Kishino, H. and Hasegawa, M. (1989).
- Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea.
J. Mol. Evol., 29:170-179.
- Klaeren, H. (1991).
- Vom Problem zum Programm.
B. G. Teubner, Stuttgart.
- Knippers, R. (1995).
- Molekulare Genetik.
Georg Thieme, Stuttgart, 6 edition.
- Knoll, A. H. (1992).
- The early evolution of eukaryotes: a geological perspective.
Science, 256:622-627.
- Kohne, D. E. (1970).
- Evolution of higher-organism DNA.
Quart. Rev. Biophys., 33:327-375.
- Kreyszig (1975).
- Statistische Methoden und ihre Anwendung.
Vandenhoeck und Ruprecht, Göttingen, 5 edition.
- Kuhner, M. K. and Felsenstein, J. (1994).
- A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.
Mol. Biol. Evol., 11:456-468.
- Lewin, B. (1994).
- Genes V.
Oxford University Press, Oxford.
- Li, W.-H. and Graur, D. (1991).
- Fundamentals of Molecular Evolution.
Sinauer Associates, Sunderland, Massachusetts.
- Lodish, H., Baltimore, D., Berk, A., Zipursky, S. L., Matsudaira, and Darnell, J. (1995).
- Molecular Cell Biology.
Scientific American Books, New York, 3 edition.
- Maddison, W. P. and Maddison, D. R. (1992).
- MacClade, Version 3.
Sinauer Associates, Sunderland, Massachusetts.
- Maier, U.-G., Hofmann, C. J. B., Eschbach, S., Wolters, J., and Igloi, G. L. (1991).
- Demonstration of nucleomorph-encoded eukaryotic small subunit ribosomal RNA in cryptomonads.
Mol. Gen. Genet., 230:155-160.
- Margulis, L. (1970).
- Origin of Eukaryotic Cells.
University Press, New Haven.
- Margulis, L. and Schwartz, K. V. (1988).
- Five Kingdoms.
Freeman and Company, New York.
- Matsuda, H., Hagstrom, R., Overbeek, R., and Kaneda, Y. (1994).
- Implementation of a parallel processing system for inference of phylogenetic trees.
unpublished.
- Mereschkowsky, C. (1905).
- Über Natur und Ursprung der Chromatophoren im Pflanzenreiche.
Biol. Zentralblatt, 25:593-604.
- Mereschkowsky, C. (1910).
- Theorien der zwei Plasmaarten als Grundlage der Symbiogenesis, einer neuen Lehre der Entstehung der Organismen.
Biol. Zentralblatt, 30:278-303.
- Nakaya, A., Yamamoto, K., and Yonezawa, A. (1995).
- RNA secondary structure prediction using highly parallel computers.
CABIOS, 11:685-692.
- Neyman, J. (1971).
- Molecular studies of evolution: a source of novel statistical problems.
In Gupta, S. S. and Yackel, J., editors, Statistical Decision Theory and Related Topics. Academic Press, New York.
- Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R. (1994a).
- fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood.
CABIOS, 10:41-48.
- Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R. (1994b).
- fastDNAml manual, version 1.0.
- Olsen, G. J., Overbeek, R., Larsen, N., Marsh, T. L., McCaughey, M., Maciukenas, M. A., Kuan, W.-M., Macke, T. J., Xing, Y., and Woese, C. R. (1992).
- The ribosomal database project.
Nucleic Acids Res., 20:2199-2200.
- Olsen, G. J. and Woese, C. R. (1993).
- Ribosomal RNA: a key to phylogeny.
FASEB J., 7:113-123.
- Oram, A. and Talbott, S. (1991).
- Managing Projects with make.
O'Reilly and Associates, Sebastopol, 2 edition.
- Ottmann, T. and Widmayer, P. (1993).
- Algorithmen und Datenstrukturen.
BI Wissenschaftsverlag, Mannheim.
- Press, W. H., Flannery, B. P., Teukolsky, S. A., and Vetterling, W. T. (1988).
- Numerical Recipes in C: The Art of Scientific Computing.
Cambridge University Press, Cambridge.
- Rice, C. M., Fuchs, R., Higgins, D. G., Stoehr, P. J., and Cameron, G. N. (1993).
- The EMBL data library.
Nucleic Acids Res., 21:2967-2971.
- Rosenblatt, B. (1993).
- Learning the Korn Shell.
O'Reilly and Associates, Sebastopol.
- Saccone, C., Gissi, C., Lanave, C., and Pesole, G. (1995).
- Molecular classification of living organisms.
J. Mol. Evol., 40:273-279.
- Saitou, N. and Nei, M. (1987).
- The neighbor-joining method: A new method for reconstructing phylogenetic trees.
Mol. Biol. Evol., 4:406-425.
- Sanger, F., Nicklen, S., and Coulsen, A. R. (1977).
- DNA sequencing with chain-terminating inhibitors.
Proc. Natl. Acad. Sci. USA, 74:5463-5467.
- Schneider, H.-J., editor (1991).
- Lexikon der Informatik und Datenverarbeitung.
Oldenbourg Verlag, München.
- Stryer, L. (1988).
- Biochemistry.
Freeman and Company, New York.
- Swofford, D. L. and Olsen, G. J. (1990).
- Phylogeny reconstruction.
In Hillis, D. M. and Moritz, C., editors, Molecular Systematics. Sinauer Associates, Sunderland, Massachusetts.
- Tillier, E. R. M. and Collins, R. A. (1995).
- Neighbor joining and maximum likelihood with RNA sequences: Addressing the interdependence of sites.
Mol. Biol. Evol., 12:7-15.
- Van de Peer, Y., Van den Broeck, I., and De Wachter, R. (1994).
- Database on structure of small ribosomal subunit RNA sequences.
Nucleic Acids Res., 22:3488-3494.
- Van de Peer, Y., Van der Auwera, G., and De Wachter, R. (1996).
- The evolution of stramenopiles and aveolates as derived by ''substitution rate calibration`` of small ribosomal subunit RNA.
J. Mol. Evol., 42:000-000.
in press.
- Vingron, M. (1995).
- Deutsches Krebsforschungszentrum, Heidelberg.
Personal communication.
- Vingron, M. and von Haeseler, A. (1994).
- Towards integration of multiple alignment and phylogenetic tree construction.
Arbeitspapiere der GMD 852, Gesellschaft für Mathematik und Datenverarbeitung, Sankt Augustin.
- Wainright, P. O., Hinkle, G., Sogin, M. L., and Stickel, S. K. (1993).
- Monophyletic origins ot the metazoa: An evolutionary link with fungi.
Science, 260:340-342.
- Wall, L. and Schwartz, R. L. (1991).
- Programming perl.
O'Reilly and Associates, Sebastopol.
- Waterman, M. S. (1995).
- Introduction to Computational Biology.
Chapman and Hall, London.
- Watson, J. D. (1990).
- The Human Genome Project: Past, present, and future.
Science, 248:44-49.
- Watson, J. D., Gilman, M., Witkowski, J., and Zoller, M. (1992).
- Recombinant DNA.
Freeman and Company, New York, 2 edition.
- Weberling, F. and Stützel, T. (1993).
- Biologische Systematik.
Wiss. Buchges., Darmstadt.
- Wehner, R. and Gehring, W. (1995).
- Zoologie.
Georg Thieme Verlag, Stuttgart, 23 edition.
- Weir, B. S., editor (1990).
- Genetic Data Analysis.
Sinauer Associates, Sunderland, Massachusetts.
- Yang, Z., Goldman, N., and Friday, A. (1994).
- Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation.
Mol. Biol. Evol., 11:316-324.
Heiko Schmidt
7/17/1997