2.9: Bibliography

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[1] Thomas H. Cormen, Charles E. Leiserson, Ronald L. Rivest, and Clifford Stein. Introduction to Algo- rithms. The MIT Press, London, third edition, 1964.

[2] Paolo Di Tommaso, Sebastien Moretti, Ioannis Xenarios, Miquel Orobitg, Alberto Montanyola, Jia-Ming Chang, Jean-Fran ̧cois Taly, and Cedric Notredame. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Research, 39(Web Server issue):W13–W17, 2011.

[3] Robert C Edgar. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research, 32(5):1792–7, January 2004.

[4] D F Feng and R F Doolittle. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. Journal of Molecular Evolution, 25(4):351–360, 1987.

[5] Kazutaka Katoh, George Asimenos, and Hiroyuki Toh. Multiple alignment of DNA sequences with MAFFT. Methods In Molecular Biology Clifton Nj, 537:39–64, 2009.

[6] John D. Kececioglu and David Sankoff. Efficient bounds for oriented chromosome inversion distance. In Proceedings of the 5th Annual Symposium on Combinatorial Pattern Matching, CPM ’94, pages 307–325, London, UK, UK, 1994. Springer-Verlag.

[7] Manolis Kellis. Dynamic programming practice problems. http://people.csail.mit.edu/bdean/6.046/dp/, September 2010.

[8] Manolis Kellis, Nick Patterson, Matthew Endrizzi, Bruce Birren, and Eric S Lander. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, 423(6937):241–254, 2003.

[9] Timo Lassmann and Erik L L Sonnhammer. Kalign–an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics, 6(1):298, 2005.

[10] Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes S ̈oding, Julie D Thompson, and Desmond G Higgins. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7(539):539, 2011.

[11] Zhaolei Zhang and Mark Gerstein. Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Research, 31(18):5338–5348, 2003.