Difference between revisions of "Dr. Rasmus Nielsen Laboratory"

Revision as of 19:41, 28 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

• Taxonomy (from GenBank files)
• ClustalW/X (align top 50; ignore E-value; remove redundancy)
  • clustalw all.fsa
  • clustalx all.aln
  • NJplot (i.e. njplot all.ph)
• MrBayes
  • Bayesian inference
  • Phylogenetics
  • Bayesian Phylogenetic Analysis
  • Markov chain Monte Carlo
  • NEXUS file format
• Find probability of each group

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

• PLANTS Database — by the USDA
• Wikispecies

ClustalW

• ClustalW

MrBayes

• MrBayes: Bayesian Inference of Phylogeny — Official Homepage
• MrBayes Wiki — ('Christoph')

Misc

• Phalaris arundinacea

References

• Molecular Evolution papers