Phylogenetic Tree Building Methods - Bioinformatics: A Swiss Perspective - page 352

5. Edgar RC. (2004) MUSCLE: a multiple sequence alignment method with
reduced time and space complexity. BMC Bioinformatics 5 : 113.
6. Sokal RR, Michener CD. (1958) Statistical method for evaluating systematic
relationships. Univ Kans Sci Bull 38 : 1409-38.
7. Sankoff D. (1975) Minimal mutation trees of sequences. SIAM J Appl Math 28
35-42.
8. Redelings BD, Suchard MA. (2005) Joint Bayesian estimation of alignment and
phylogeny. Syst Biol 28 (3): 401-18.
9. Lunter G, Miklos I, Drummond A et al . (2005) Bayesian coestimation of
phylogeny and sequence alignment. BMC Bioinformatics 6 : 83.
10. Bourque G, Pevzner P. (2002) Genome-scale evolution: reconstructing gene
orders in the ancestral species. Genome Res 12 (1): 26-36.
11. Moret BM, Wyman S, Bader D et al . (2001) A new implementation and detailed
study of breakpoint analysis. Pac Symp Biocomput (2001): 583-94.
12. Day W, Johnson D, Sankoff D. (1986) The computational complexity of infer-
ring rooted phylogenies by parsimony. Math Biosci 81 : 33-42.
13. Day WHE. (1987) Computational complexity of inferring phylogenies from
dissimilarity matrices. Bull Math Biol 49 (4) 461-7.
14. Chor B, Tuller T. (2006) Finding a maximum likelihood tree is hard. J ACM
53 (5): 722-44.
15. Cox DR. (2006) Frequentist and Bayesian statistics: a critique. In: Proceedings of
PHYSTAT 05 . London, UK: Imperial College Press, pp. 3-6.
16. Bergsten, J. (2005) A review of long-branch attraction. Cladistics 21 (2): 163-93.
17. Fitch WM, Margoliash E. (1967) Construction of phylogenetic trees. Science
155 : 279-84.
18. Rzhetsky A, Nei M. (1993) Theoretical foundation of the minimum evolution
method of phylogenetic inference. Mol Biol Evol 10 : 1073-95.
19. Saitou N, Nei M. (1987) The neighbor-joining method: a new method for
reconstructing phylogenetic trees. J Mol Evol 4 : 406-25.
20. Gascuel O. (1997) BIONJ: an improved version of the NJ algorithm based on
a simple model of sequence data. Mol Biol Evol 14 (7): 685-95.
21. Bruno WJ, Socci ND, Halpern AL. (2000) Weighted neighbor joining: a likelihood-
based approach to distance-based phylogeny reconstruction. Mol Biol Evol 17 (1):
189-97.
22. Felsenstein J. (1987) Cases in which parsimony and compatibility methods will
be positively misleading. Syst Zool 27 : 401-10.
23. Yang Z. (2007) PAML 4: Phylogenetic analysis by maximum likelihood.
Mol Biol Evol 24 (8): 1586-91.
24. Guindon S, Gascuel O. (2003) A simple, fast, and accurate algorithm to estimate
large phylogenies by maximum likelihood. Syst Biol 52 (5): 696-704.
25. Stamatakis A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic
analyses with thousands of taxa and mixed models. Bioinformatics 22 (21): 2688-90.