Difference between revisions of "Dr. Rasmus Nielsen Laboratory"

From Christoph's Personal Wiki
Jump to: navigation, search
(Overview of research: clustalw)
 
(21 intermediate revisions by the same user not shown)
Line 1: Line 1:
'''[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.
+
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.
  
==Professor Information==
+
== Research topics ==
* '''Rasmus Nielsen''' (Ole Roemer Fellow)
+
* [[:Category:Phylogenetics|Phylogenetics]]
* Office: 314
+
* [[MrBayes]]
* Phone: +45 3532 1279
+
* [[Clustal]]
* E-mail: rasmus@binf.ku.dk
+
* [[BLAST]]
  
==Overview of research==
+
== External links ==
 
+
===Taxonomy===
* Taxonomy (from GenBank files)
+
* [http://plants.usda.gov/ PLANTS Database] — by the USDA
* ClustalW (align top 50; ignore ''E''-value; remove redundancy)
+
** clustalw all.fsa
+
** clustalx all.aln
+
** njplot all.ph
+
* MrBayes
+
* Find probability of each group
+
 
+
Nucleotide model: GTR (option: +gamma)
+
Constrain all phylogenetic groups to be monophyletic
+
Make option: strict clock trees (uniform) (prset brlenspr=clock:uniform)
+
 
+
1,000,000 updates (e.g. cycles)
+
discard first 50,000 as burn-in
+
sample a total of 10,000 trees (say)
+
 
+
Then process output to get probabilities of each possible phylogenetic assignment of query sequence.
+
 
+
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.
+
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).
+
Remember, MrBayes will output the probabililities of specific groups (or partitions) directly.
+
So you don't have to do anything with trees yourself.
+
 
+
==External links==
+
 
* [http://species.wikipedia.org/wiki/Main_Page Wikispecies]
 
* [http://species.wikipedia.org/wiki/Main_Page Wikispecies]
 +
===ClustalW===
 
* [http://www.ebi.ac.uk/clustalw/ ClustalW]
 
* [http://www.ebi.ac.uk/clustalw/ ClustalW]
 +
===MrBayes===
 
* [http://mrbayes.csit.fsu.edu/index.php MrBayes: Bayesian Inference of Phylogeny] — Official Homepage
 
* [http://mrbayes.csit.fsu.edu/index.php MrBayes: Bayesian Inference of Phylogeny] — Official Homepage
 
* [http://mrbayes.csit.fsu.edu/wiki/index.php/Main_Page MrBayes Wiki] — ('Christoph')
 
* [http://mrbayes.csit.fsu.edu/wiki/index.php/Main_Page MrBayes Wiki] — ('Christoph')
 +
===Misc===
 +
* [http://arctos.database.museum/TaxonomyResults.cfm?full_taxon_name=Phalaris%20arundinacea ''Phalaris arundinacea'']
 +
===References===
 +
* [http://workshop.molecularevolution.org/resources/references/ Molecular Evolution papers]
 +
===Misc===
 +
* [[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