Difference between revisions of "Dr. Rasmus Nielsen Laboratory"

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'''[http://www.binf.ku.dk/~rasmus/webpage/ras.html Dr. Rasmus Nielsen Laboratory]''' is where I am currently doing research (December 2005-present). It is located at the ''[http://www.binf.ku.dk/view/Main Centre for Bioinformatics]'', [http://www.ku.dk/ København Universitet], Denmark.
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The '''[http://www.binf.ku.dk/~rasmus/webpage/ras.html Dr. Rasmus Nielsen Laboratory]''' is where I did research from December 2005-February 2006). It is located at the ''[http://www.binf.ku.dk/ Centre for Bioinformatics]'', [http://www.ku.dk/ København Universitet], Denmark.
  
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==Professor Information==
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== Research topics ==
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* '''Rasmus Nielsen''' (Ole Roemer Fellow)
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* [[:Category:Phylogenetics|Phylogenetics]]
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* Office: 314
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* [[MrBayes]]
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* Phone: +45 3532 1279
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* [[Clustal]]
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* E-mail: rasmus@binf.ku.dk
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* [[BLAST]]
  
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==Overview of research==
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== External links ==
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* '''Taxonomy''' (from GenBank files)
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* '''ClustalW/X''' (align top 50; ignore ''E''-value; remove redundancy)
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** <tt>clustalw all.fsa</tt>
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** <tt>clustalx all.aln</tt>
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** [[NJplot]] (i.e. <tt>njplot all.ph</tt>)
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* '''[[MrBayes]]'''
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** [[Bayesian inference]]
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** [[Phylogenetics]]
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** [[Bayesian Phylogenetic Analysis]]
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** [[Markov chain Monte Carlo]]
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** [[NEXUS file format]]
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* '''Find probability of each group'''
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==Test runs==
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* Nucleotide model: '''General Time Reversible''' ('''GTR''') (option: +gamma): <tt>lset nst=2 rates=gamma</tt>
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* ('''Do not do the following!''') Constrain all phylogenetic groups to be monophyletic.
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* Make option: <tt>strict clock trees</tt> (uniform) (<tt>prset brlenspr=clock:uniform</tt>)
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* 1,000,000 updates (e.g. cycles)
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* discard first 50,000 as burn-in
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* sample a total of 10,000 trees (say)
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* Then process output to get probabilities of each possible phylogenetic assignment of query sequence.
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In MrBayes, if you run the program with the constraints of monophyletic groups, you are forcing the query sequence '''not''' to be part of these groups. So that won't work.
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Instead, run it without the constraints and simply check how often the query sequence is member of a partition that only contains one particular phylogenetic group as members (at any phylognetic level, e.g. species, genus, family, order, etc).
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Remember, MrBayes will output the probabililities of specific groups (or partitions) directly. So you don't have to do anything with trees yourself.
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==External links==
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===Taxonomy===
 
===Taxonomy===
 
* [http://plants.usda.gov/ PLANTS Database] &mdash; by the USDA
 
* [http://plants.usda.gov/ PLANTS Database] &mdash; by the USDA
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===References===
 
===References===
 
* [http://workshop.molecularevolution.org/resources/references/ Molecular Evolution papers]
 
* [http://workshop.molecularevolution.org/resources/references/ Molecular Evolution papers]
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===Misc===
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* [[Dr. Rasmus Nielsen Laboratory/Notes]]
  
 
[[Category:Academic Research]]
 
[[Category:Academic Research]]

Latest revision as of 15:39, 5 July 2012

The Dr. Rasmus Nielsen Laboratory is where I did research from December 2005-February 2006). It is located at the Centre for Bioinformatics, København Universitet, Denmark.

Research topics

External links

Taxonomy

ClustalW

MrBayes

Misc

References

Misc

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