treebuilding.pdf
CIS 410/510 Bioinformatics |
| Introduction | ||
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Hunter93.pdf | "Molecular Biology for Computer Scientists", by Larry Hunter (Artificial Intelligence and Molecular Biology, MIT Press, 1993). |
| Pairwise Alignment | ||
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Giegerich96.pdf | "Pairwise Sequence Alignment", by Robert Giegerich and David Wheeler. |
| Multiple Alignment | ||
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Phillips00.pdf | "Multiple Sequence Alignment in Phylogenetic Analysis", by A. Phillips, et al, Molecular Phylogenetics and Evolution 16(3), 2000. |
| Phylogenetic Trees | ||
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treeterm.pdf
treebuilding.pdf |
"Trees and Their Terms" and "Introduction to Tree Building", excerpts from Molecular Evolution: A Phylogenetic Approach, by R. Page and E. Holmes, Blackwell Science, 1998. |
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Martin99.pdf | "Mosaic bacterial chromosomes: a challenge en route to a tree of genomes", by William Martin, BioEssays, 1999. |
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Huelsenbeck02.pdf | "Potential Applications and Pitfalls of Bayesian Inference of Phylogeny", by John Huelsenbeck, et al, Syst.Biol. 51(5):673–688, 2002. |
| Gene Finders | ||
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Burge98.pdf | "Finding the Genes in Genomic DNA", by Christopher Burge and Samuel Karlin, Current Opinion in Structural Biology, 1998. |
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Haussler98.pdf | "Computational Genefinding", by David Haussler (long version of paper from Trends in Biochemical Sciences, Supplementary Guide to Bioinformatics, 1998) |
| National Center for Biotechnology Information (NCBI) | ||
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http://ncbi.nih.gov | Home page. |
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Science Primer | An introduction to the field of bioinformatics and short papers on genomics, phylogenetics, and other topics covered in this course. |
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ftp://ftp.ncbi.nih.gov/genomes | FTP directory of complete genomes. |
| Bioinformatics Applications | ||
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Phylogeny Programs | A list of phylogenetic inference applications, maintained by Joe Felsenstein at the University of Washington. |
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CLUSTAL X | Multiple sequence alignment and phylogenetic inference using the neighbor-joining method. |
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Treeview X | Program to display phylogenetic trees; runs on Mac (including OS/X), Unix, Windows). |
| Programming Languages | ||
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Programming Languages Examples Alike Cookbook | Code examples from the Perl Cookbook, with some examples shown in other languages. |
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WWW C++ Information | A great set of links put together by Bernd Mohr, former postdoc in Al Malony's lab. |
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C/C++ Reference | Quick reference guide to C++ STL (caveat emptor). |
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Perl Mongers | Unofficial Perl home page; lots of links to on-line info. |
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PHP Home Page | Downloads, manuals, .... |
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MySQL Home Page | Downloads, manuals, .... |
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