User: dieter

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dieter0
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Posts by dieter

<prev • 14 results • page 1 of 2 • next >
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Pre-Testing for Site Specific Rate Model (SSR) or Codon Model for protein coding of an MSA
... Hello all, I have the following problem: I have an analysis with some DNA partitions, some indel partitons and 2 partitions of protein coding DNA regions. Now I wanted to test BEFORE I run the final calculation with all partitions (in MrBayes) if it is better to use a site specific rate model (SSR) ...
alignment rna-seq written 6 weeks ago by dieter0
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Will "empty" sequences in an MSA change the best fit model?
... Hello all, I have a simple question where I did not find an answer, yet - explained with an example: Assuming one has an aligment, consisting of 2 partitions, and at the second partition sequences are not available, so that these lines are filled with "-" or "?" only. And then one makes a best fit m ...
sequence alignment written 6 weeks ago by dieter0
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Comment: C: Shape parameter of the gamma distribution of rate variation
... Hello Kevin, I checked it again and: You are right! It is exactly how you said. I found the proof here: http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Phylogenetics:_MrBayes_Lab It is the exponetial distribution and tha parameter is no longer alpha but lambda. The interesting thing is that the ...
written 11 weeks ago by dieter0
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Comment: C: Shape parameter of the gamma distribution of rate variation
... Thanks Natasha, But I'm sorry, the pdf only describes the gamma distribution (which I already know) - all is clear there - but it does not answr my questions. The second link leads to a discussion about the Invar Model - this has nothing to do with my question. But thanks anyway. All the best Dieter ...
written 11 weeks ago by dieter0
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Shape parameter of the gamma distribution of rate variation
... Hello all, I have another question for the experts where I did not find any answer, yet. It's about the shape parameter of the gamma distribution of rate variation. Known as Alpha. I know what the parameter is, and I know that if when Alpha = 1 the gamma distribution matches the exponential distribu ...
sequence written 11 weeks ago by dieter0 • updated 11 weeks ago by natasha.sernova2.8k
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Indel-partition settings for MrBayes
... Hello all, I set up an analysis with Mr bayes with a DNA partition and an indel-partition (binary) I obtained from Fastgap. I set MrBayes as suggeted in the manual (here example): Format datatype=mixed(dna:1-1000,restriction:1001-1200) and for the Indel-partition: lset app=(2) coding=vari ...
sequence alignment written 11 weeks ago by dieter0
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Comment: A: Deleting constant site columns OK?
... Thank you ymaule and jrj.healey, Yes, I use the MSA for MrBayes and RAxML to compute phylogenetic trees. OK, that helps - I also thought that way but found very different answers. If someone has more information or hints, please let me (and others) know. Thanks Dieter ...
written 11 weeks ago by dieter0
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Deleting constant site columns OK?
... Hello all, I have another beginner question: Is it true, that in an MSA 100% constant positions (columns which only contain the same nucleotide or amino acid in all sequences and no gaps) can be deleted from the alignment without losing any phylogenetic information? Thanks Dieter ...
phylogeny alignment homology written 12 weeks ago by dieter0
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Comment: C: Gaps in Protein coding Sequenzes allowed?
... Thank you Jean-Karim, That answers my questin. All the best Dieter ...
written 12 weeks ago by dieter0
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Answer: A: Gaps in Protein coding Sequenzes allowed?
... Thank you very much Jean-Karim, You wrote it depends to the context - that means some protein coding sequences can contain singel gaps in codons and some not. Right? So, how can I find out if one special region can contain gaps or not? In many studys I have the beta-tub gene (Exon 5 to 6) and the ef ...
written 3 months ago by dieter0

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