Difference between revisions of "Dr. Rasmus Nielsen Laboratory"

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(→‎Overview of research: link to "MrBayes")
(Added "Test runs")
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* '''Find probability of each group'''
 
* '''Find probability of each group'''
  
−
Nucleotide model: GTR (option: +gamma)
+
==Test runs==
−
Constrain all phylogenetic groups to be monophyletic
+
−
Make option: strict clock trees (uniform) (prset brlenspr=clock:uniform)
+
  
−
1,000,000 updates (e.g. cycles)
+
* Nucleotide model: '''General Time Reversible''' ('''GTR''') (option: +gamma): <tt>lset nst=2 rates=gamma</tt>
−
discard first 50,000 as burn-in
+
* ('''Do not do the following!''') Constrain all phylogenetic groups to be monophyletic.
−
sample a total of 10,000 trees (say)
+
* Make option: <tt>strict clock trees</tt> (uniform) (<tt>prset brlenspr=clock:uniform</tt>)
  
−
Then process output to get probabilities of each possible phylogenetic assignment of query sequence.
+
* 1,000,000 updates (e.g. cycles)
 +
* discard first 50,000 as burn-in
 +
* sample a total of 10,000 trees (say)
  
−
In MrBayes - if you run the program with the constraints of monophyletic groups -
+
* Then process output to get probabilities of each possible phylogenetic assignment of query sequence.
−
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  
+
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.
−
member of a partition that only contains one particular phylogenetic group as members  
+
 
−
(at any phylognetic level, e.g. species, genus, family, order, etc).
+
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.
+
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==
 
==External links==

Revision as of 18:37, 27 December 2005

Dr. Rasmus Nielsen Laboratory is where I am currently doing research (December 2005-present). It is located at the Centre for Bioinformatics, København Universitet, Denmark.

Professor Information

  • Rasmus Nielsen (Ole Roemer Fellow)
  • Office: 314
  • Phone: +45 3532 1279
  • E-mail: rasmus@binf.ku.dk

Overview of research

Test runs

  • Nucleotide model: General Time Reversible (GTR) (option: +gamma): lset nst=2 rates=gamma
  • (Do not do the following!) 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

Taxonomy

ClustalW

MrBayes

Misc

References

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