Algoritmer for evolutionære træer, forår 2005
seneste opdatering: 16.03.05
Forelæsere
Pawel Winter (kursusansvarlig)
Martin Zachariasen
David Pisinger
Benny Nielsen
Anna Ostlin
Inge Li Gørtz
Phillip Bille
- Plancher til Pawel's 1. forelæsning: LINK
- Litteratur til Pawel's 1. forelæsning
- J. Setubal and J. Meidanis, Introduction to Computational Biology, kap. 3.
- D.W. Mount, Bioinformatics, kap. 7
- Plancher til Martin's forelæsning: LINK
- Litteratur til Martin's forelæsning
- T. Jiang, L. Wang, Algorithmic Methods for Multiple Sequence Alignment, 2002.
- L. Wang, D. Gusfield, Improved Approximation Algorithms for Tree
Alignment, Journal of Algorithms 25, 255-273, 1997. http://dx.doi.org/10.1006/jagm.1997.0882
- Opgave til Pawel's og Martin's forelæsninger: LINK.
- Plancher til Pawel's 2. forelæsning: LINK
- Litteratur til Pawel's 2. forelæsning
- J. Setubal and J. Meidanis, Introduction to Computational Biology, kap. 6.
- M. Farach, S. Kannan and T. Warnow, A robust model for finding optimal evolutionary trees, Algorithmica 13 (1995) 155-179.
- Opgave til Pawel's 2. forelæsning: LINK.
- Plancher til Benny's forelæsning: LINK
- Litteratur til Benny's forelæsning
- B. Schwikowski and M. Vingron. Weighted sequence graphs:
boosting iterated dynamic programming using locally suboptimal
solutions. Discrete Applied Mathematics, 127(1):95, 2003.
http://dx.doi.org/10.1016/S0166-218X(02)00288-3
- J. Hein. A new method that simultaneously aligns and reconstructs
ancestral sequences for any number of homologous sequences, when
the phylogeny is given. Molecular Biology and Evolution, 6:649,
1989.
- Opgave til Benny's forelæsning: LINK
- Plancher til Anna's forelæsning: LINK
- Litteratur til Anna's forelæsning
- Computing the Quartet Distance between Evolutionary Trees in Time O(n log n), by Brodal, Fagerberg, and Pedersen, Algorithmica (2004) 38: 377-395.
- Conference version, with extra log n-factor: Computing the Quartet Distance between Evolutionary Trees in Time O(n log^2 n),
by Brodal, Fagerberg, and Pedersen, ISAC 2001.
Studerende
- Jonas Christian Drewsen (drewsen(a)diku.dk): xxxooo
- Christian Edinger Munk Plum (christianpl(a)m2.stud.ku.dk): xoxxxx
- Anders Schack-Nielsen (anderssn(a)diku.dk): xxxxxx
- Stine Søndergaard (stines(a)diku.dk): xxxxx+
- Mads Jepsen (di04i018(a)diku.dk): xxoooo
- Sune Christiansen (sunejens(a)diku.dk): oxxooo