lutteropp
Verification of the partitioned MSA generated by using SeqGen
Because of problems that emerged with the "small_network" experiments (NetRAX inferring a 0-reticulation network that has better loglikelihood than the "true" simulated network on the simulated MSA data), I have decided that we need to double-check the simulated MSA.
Proposed verification experiment A:
- Use raxml-ng on each partition of the MSA generated by seq-gen
- For each raxml-ng-on-partition-belonging-to-a-displayed-tree run, check if raxml-ng indeed inferred that displayed tree.
Proposed verification experiment B:
- Create MSAs for each displayed tree in separate SeqGen calls.
- Merge these MSAs into one big partitioned MSA by hand.
- Re-run NetRAX on such a dataset.
- Verify that again the BIC sees no supporting signal for reticulations.
very good verification setup
On 01.12.20 16:21, Sarah Lutteropp wrote:
Because of problems that emerged with the "small_network" experiments (NetRAX inferring a 0-reticulation network that has better loglikelihood than the "true" simulated network on the simulated MSA data), I have decided that we need to double-check the simulated MSA.
Proposed verification experiment A:
- Use raxml-ng on each partition of the MSA generated by seq-gen
- For each raxml-ng-on-partition-belonging-to-a-displayed-tree run, check if raxml-ng indeed inferred that displayed tree.
Proposed verification experiment B:
- Create MSAs for each displayed tree in separate SeqGen calls.
- Merge these MSAs into one big partitioned MSA by hand.
- Re-run NetRAX on such a dataset.
- Verify that again the BIC sees no supporting signal for reticulations.
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-- Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
www.exelixis-lab.org
other suggestion: take a network with one reticulation and inheritance probs of around 0.5 for each of the reticulated branches and generate a MSA of length 1000, 2000 etc and see how the BIC evolves
That's a good additional approach, I would not disregard the other two though ...
On 02.12.20 10:42, celinescornavacca wrote:
other suggestion: take a network with one reticulation and inheritance probs of around 0.5 for each of the reticulated branches and generate a MSA of length 1000, 2000 etc and see how the BIC evolves
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-- Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
www.exelixis-lab.org