User: UBodenhofer

gravatar for UBodenhofer
UBodenhofer250
Reputation:
250
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Trusted
Location:
Johannes Kepler University, Linz, Austria
Website:
http://www.bioinf.jku.at/
Twitter:
u_bode
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Google Scholar Page
Last seen:
2 weeks ago
Joined:
5 years, 11 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 • 44 results • page 1 of 5 • next >
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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 14 days 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 6 weeks 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 7 weeks ago by UBodenhofer250
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Comment: C: Using msa msaPrettyPrint(): saving multiple alignement fasta file
... Since you cannot run texi2dvi() itself, the problem is not within the 'msa' package. You either have no TeX/LaTeX system installed or it is improperly installed (e.g. the execution paths are not correctly set). I suggest you open a shell/command prompt window, change to the directory  '~/Desktop/' a ...
written 8 weeks ago by UBodenhofer250
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Comment: C: Using msa msaPrettyPrint(): saving multiple alignement fasta file
... I can only speculate. Maybe try the following: run msaPrettyPrint() with 'output="tex"' and then run texi2pdf() (from the 'tools' package) on that file. That's basically what msaPrettyPrint() does too. If that does not work, then I'll have to look into my package's code. If it does not work either, ...
written 4 months ago by UBodenhofer250
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Answer: A: Status 1 error when using msaPrettyPrint() to make pdfs with MsaAAMultipleAlignm
... Seems like a LaTeX error. I see two possible sources: (1) There is a problem with your TeX system. (2) The LaTeX code created by msaPrettyPrint() cannot be processed successfully. This can happen if the alignment is too large. 101 sequences seems problematic to me, since 101 is more than the number ...
written 5 months ago by UBodenhofer250
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Answer: A: Error in .Primitive("c")(<S4 object of class "IRanges">) : could not find sym
... It seems that it is an installation issue with one of the packages 'msa' depends on. See the following related thread: Question: Error in GRanges: could not find symbol "recursive" in environment of the generic function ...
written 5 months ago by UBodenhofer250
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Answer: A: How do I extract the complete MsaAAMultipleAlignment object to a file
... Reply to question #1: The width is controlled by the global R option 'width' (in line with the print() methods in the 'Biostrings' package). So you can change the number of columns yourself. If you want to avoid this to have a global effect on your R session, you should save the current value and th ...
written 5 months ago by UBodenhofer250
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Comment: C: How do I extract the complete MsaAAMultipleAlignment object to a file
... Excellent, I'm glad you solved it. You can also set 'halfNrow' to -1 or NA, then it prints everything. ...
written 5 months ago by UBodenhofer250
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Comment: C: How do I extract the complete MsaAAMultipleAlignment object to a file
... Are you sure you have used the option 'show="complete"'? When I run my example code from above, I see everything. ...
written 5 months ago by UBodenhofer250

Latest awards to UBodenhofer

Popular Question 6 weeks ago, created a question with more than 1,000 views. For VariantAnnotation: Performance and memory issues in readVcf
Popular Question 12 months ago, created a question with more than 1,000 views. For Problem reading VCF file using readVcf from package VariantAnnotation
Scholar 12 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 12 months ago, voted at least 25 times.
Scholar 16 months ago, created an answer that has been accepted. For A: Outputting a multiple alignment to file error: could not find function write.XSt
Autobiographer 2.0 years ago, has more than 80 characters in the information field of the user's profile.

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