User: UBodenhofer

gravatar for UBodenhofer
UBodenhofer250
Reputation:
250
Status:
Trusted
Location:
Johannes Kepler University, Linz, Austria
Website:
http://www.bioinf.jku.at/
Twitter:
u_bode
Scholar ID:
Google Scholar Page
Last seen:
2 months, 3 weeks ago
Joined:
6 years, 10 months ago
Email:
b*********@bioinf.jku.at

Associate Professor in Bioinformatics at Johannes Kepler University, Linz, Austria. Maintainer of the following packages: 'msa', 'kebabs', 'procoil', 'podkat' (Bioconductor) / 'apcluster', 'rococo' (CRAN)

Posts by UBodenhofer

<prev • 51 results • page 1 of 6 • next >
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Comment: C: visualizing alignment without realignment
... I am not 100% sure what you are asking for. My interpretation of "matching letters" is that `shadingMode="identical"` should do the job. If the issue is rather that `N` is treated like a regular character, my suggestion is simple: replace all `N`'s with dashes. If you need more custom functionality, ...
written 12 weeks ago by UBodenhofer250
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Comment: C: visualizing alignment without realignment
... Sorry, I cannot determine the source of the problem. Do your sequences contain a character that LaTeX cannot handle? (this is only a wild guess) I suggest you send me the input file and the TeX file via a private message (bodenhofer_at_bioinf.jku.at) and I will try to go deeper into the problem. ...
written 12 weeks ago by UBodenhofer250
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Comment: C: visualizing alignment without realignment
... I suggest you change `output="pdf"` to `output="tex"` and run `pdflatex` on the resulting file `newaln.tex`, and look what error message is thrown. Unfortunately, the `texi2dvi()` function does not convey enough information about what the problem is. ...
written 12 weeks ago by UBodenhofer250
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Comment: C: visualizing alignment without realignment
... I am not 100% sure, but, as far as I know, LaTeX might have issues with underscores in file names on Windows. Please try a different name of the object without an underscore character and let me know if that fixes the problem. ...
written 12 weeks ago by UBodenhofer250
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Answer: A: visualizing alignment without realignment
... Yes, it is true that `msa()` performs a multiple alignment on a set of unaligned sequences. If the sequences are indeed unaligned, there is no way to create a multiple alignment object without alignment. If the sequences are aligned (at least weakly in the sense that they all have the same lengths, ...
written 12 weeks ago by UBodenhofer250
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Answer: A: Error: could not find function "msaConvert"
... Well, as obvious from your sessionInfo() results, you are using R 3.2.4 which is more than two years old. Since Bioconductor binds releases to the latest R version, you only have Bioconductor 3.3, which includes 'msa' version 1.2.1. The msaConvert() function has been introduced in 'msa' version 1.3. ...
written 10 months ago by UBodenhofer250
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Comment: C: Error: could not find function "msaConvert"
... I have seen such error messages in the past, and the reason was always that the users read the manual of a newer version than they actually used. So, if you have the latest version, this is a new issue that I will be glad to go into. Please provide a minimal example that produces that error along wi ...
written 10 months ago by UBodenhofer250
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Comment: C: Defining populations in a msaClustalOmega alignment
... Sorry, but I don't get the question. I don't know RAxML, but it seems this is not an 'msa' issue, but a matter of how RAxML expects information about populations. Once you have found that out, you can simply change the sequence names in the FASTA file containing the alignment (if that is what RAxML ...
written 11 months ago by UBodenhofer250
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Answer: A: How to get msa output in fasta format
... If you do not want to make the extra way via the msaPrettyPrint() function, you can also directly write to a FASTA file in the following way (which is actually what msaPrettyPrint() does internally; suppose 'aln' is an object containing a multiple alignment): writeXStringSet(as(unmasked(aln), "XSt ...
written 12 months ago by UBodenhofer250
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Answer: A: seqfault wiht msa
... Thanks for reporting this issue! As far as I can see, my suspicion is indeed the vast amount of data. Actually, ClustalW is not made for such excessive amounts of data. I would rather suggest to use ClustalOmega instead. If that does not work via 'msa' either, maybe the last resort is to use stand-a ...
written 12 months ago by UBodenhofer250

Latest awards to UBodenhofer

Popular Question 12 months ago, created a question with more than 1,000 views. For VariantAnnotation: Performance and memory issues in readVcf
Popular Question 24 months ago, created a question with more than 1,000 views. For Problem reading VCF file using readVcf from package VariantAnnotation
Scholar 24 months ago, created an answer that has been accepted. For A: Outputting a multiple alignment to file error: could not find function write.XSt
Supporter 24 months ago, voted at least 25 times.
Scholar 2.2 years ago, created an answer that has been accepted. For A: Outputting a multiple alignment to file error: could not find function write.XSt
Autobiographer 2.9 years ago, has more than 80 characters in the information field of the user's profile.

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