Bioinformatics Algorithms

Dynamic Programming

• http://www.cis.upenn.edu/~sahuguet/MSA/
• http://www.blc.arizona.edu/courses/bioinformatics/align.html
• http://www.cs.monash.edu.au/~lloyd/tildeStrings/Notes/DPA.html
• http://www.cs.orst.edu/~schut/cs325/dynamic.htm
• http://www.catalase.com/dprog.htm
• http://bioweb.ncsa.uiuc.edu/~bioph490/BIOPH2.html#SEQUENCE_COMP
• http://www.qucis.queensu.ca/home/cisc365/javascript/dp1/index.html

• http://bioweb.ncsa.uiuc.edu/~bioph490/dynamic_programming_demo.html
• http://www.qucis.queensu.ca/home/cisc365/365overheads.html
• http://www.qucis.queensu.ca/home/cisc365/dp/dp.p01.html
• http://www.dgp.toronto.edu/csc270/tut_dp.html
• http://queue.ieor.berkeley.edu/~jshu/knapsack/DP/dp.html
• http://mat.gsia.cmu.edu/classes/dynamic/dynamic.html
• http://www.cs.sandia.gov/~scistra/class_3

• http://levine.sscnet.ucla.edu/Econ101/dynamic.htm
• http://mat.gsia.cmu.edu/classes/stoch_dynamic/stoch_dynamic.html

• http://mat.gsia.cmu.edu/classes/dynamic/node8.html
• http://www.maths.mu.oz.au/~moshe/dp/bibl/bibliography.html
• http://cartan.gmd.de/PAPER/ismb95/ismb_html.html
• http://screwdriver.bu.edu/bibliography/dynamic_programming.htm
• http://www.norvig.com/design-patterns/
• http://tome.cbs.univ-montp1.fr/htmltxt/Doc/manual/node137.html
• http://poem.princeton.edu/~verdu/dynamic.html
• http://www.orca1.com/opushelpweb/opusDynamic_Programming.html
• http://screwdriver.bu.edu/cn760-lectures/l7/index.htm
• http://www.ms.unimelb.edu.au/~moshe/dp/dp.html
• http://mat.gsia.cmu.edu/ORCS/0255.html
• http://aae.wisc.edu/e703/notes/a13dynpr.htm
• http://bioweb.pasteur.fr/docs/modeller/node137.html
• http://www2.uwindsor.ca/~lama/my470/ddynamic.htm
• http://students.ceid.upatras.gr/~papagel/project/ex5_6_1.htm
• http://www.cs.sunysb.edu/~algorith/lectures-good/node12.html
• http://www.cs.sunysb.edu/~algorith/lectures-good/node12.html
• http://www.utdallas.edu/~scniu/documents/7315.htm
• http://www.ii.uib.no/~pinar/seminar/larry.html
• http://www.deakin.edu.au/~gecole/books.html
• http://www.cseg.engr.uark.edu/~wessels/algs/notes/dynamic.html
• http://www.csc.liv.ac.uk/~ped/teachadmin/algor/dyprog.html
• http://www.eli.sdsu.edu/courses/fall96/cs660/notes/dynamicProg/dynamicProg.html
• http://www.cs.indiana.edu/l/www/ftp/techreports/TR514.html
• http://www.cs.brandeis.edu/~mairson/poems/node3.html

• http://www.cis.tu-graz.ac.at/igi/oaich/animations/Dynamic2.html

• http://bioweb.ncsa.uiuc.edu/~workshop/

Smith Waterman

• http://genome-www.stanford.edu/Saccharomyces/help/sw_alignment.html
• http://genome-www.stanford.edu/Saccharomyces/help/sw_details.html
• http://www.stanford.edu/~sntaylor/bioc218/final.htm
• http://www.maths.tcd.ie/~lily/pres2/sld009.htm
• http://bioweb.ncsa.uiuc.edu/~workshop/Lab_3/Smith-Waterman.htm
• http://www.tigem.it/LOCAL/SW/threshold.html
• http://sgbcd.weizmann.ac.il/genweb/help/smith-waterman.html
• http://cbrg.ethz.ch/ServerBooklet/section2_3_5.html

Needleman & Wunsch

• http://www.maths.tcd.ie/~lily/pres2/sld003.htm
• http://acer.gen.tcd.ie/~amclysag/nwswat.html
• http://www.nada.kth.se/~erikw/thesis/chapter2_3.html
• http://www.irbm.it/irbm-course95/gb/docs/amps/subsection3_6_1.html
• http://www.ibc.wustl.edu/~zuker/Bio-5495/align-html/node3.html

General (NW vs. SW vs. HMM, etc.)

• http://www.maths.tcd.ie/~lily/pres2/
• http://acer.gen.tcd.ie/~amclysag/nwswat.html
• http://laguerre.psc.edu/biomed/TUTORIALS/SEQUENCE/MULTIPLE/tutorial.html
• http://www.cse.ucsc.edu/research/compbio/

Hmms

• http://www.medmicro.mds.qmw.ac.uk/HMMER/main.html
• http://alfredo.wustl.edu/ismb96/abs/p02.html
• http://www.cse.ucsc.edu/research/compbio/html_format_papers/hughkrogh96/cabios.html
• http://wwwsyseng.anu.edu.au/~jason/hmmlinks.html
• http://www.breadfan.com/markov.html
• http://cslu.cse.ogi.edu/HLTsurvey/ch1node34.html
• http://www.ibc.wustl.edu/service/hmmalign/glocal.html
• http://www.cse.ucsc.edu/research/compbio/html_format_papers/ismb94/node5.html
• http://www.iscs.nus.edu.sg/~luakt/ic3222/lecture/nlp18new/index.htm

• http://www.cse.ucsc.edu/research/compbio/sam.html SAM Software for HMMs

Genetic Algorithms

• http://www.staff.uiuc.edu/~carroll/ga.html
• http://kal-el.ugr.es/gags.html
• http://kal-el.ugr.es/~jmerelo/GAJS.html