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lutteropp / NetRAX

Phylogenetic Network Inference without ILS
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Verification of the partitioned MSA generated by using SeqGen #21

Open lutteropp opened 3 years ago

lutteropp commented 3 years ago

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:

  1. Use raxml-ng on each partition of the MSA generated by seq-gen
  2. 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:

  1. Create MSAs for each displayed tree in separate SeqGen calls.
    1. Merge these MSAs into one big partitioned MSA by hand.
    2. Re-run NetRAX on such a dataset.
    3. Verify that again the BIC sees no supporting signal for reticulations.
stamatak commented 3 years ago

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:

  1. Use raxml-ng on each partition of the MSA generated by seq-gen
  2. 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:

  1. Create MSAs for each displayed tree in separate SeqGen calls.
  2. Merge these MSAs into one big partitioned MSA by hand.
  3. Re-run NetRAX on such a dataset.
  4. 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

celinescornavacca commented 3 years ago

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

stamatak commented 3 years ago

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

celinescornavacca commented 3 years ago

Yep, it is an additional one, if it was not clear