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''' (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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** <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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Nucleotide model: GTR (option: +gamma)
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Constrain all phylogenetic groups to be monophyletic
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Make option: strict clock trees (uniform) (prset brlenspr=clock:uniform)
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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 -
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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
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member of a partition that only contains one particular phylogenetic group as members
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(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.
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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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===Misc===
 
===Misc===
 
* [http://arctos.database.museum/TaxonomyResults.cfm?full_taxon_name=Phalaris%20arundinacea ''Phalaris arundinacea'']
 
* [http://arctos.database.museum/TaxonomyResults.cfm?full_taxon_name=Phalaris%20arundinacea ''Phalaris arundinacea'']
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===References===
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* [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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