User: ulrich.bodenhofer

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Austria
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6 months ago
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4 years, 3 months ago
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u****************@gmail.com

Posts by ulrich.bodenhofer

<prev • 4 results • page 1 of 1 • next >
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Answer: A: Can any of the existing `MSA` packages be used/adapted to visualize a pre-aligne
... It is quite straightforward to read a file with a pre-computed alignment. Suppose the file '`myAln.txt`' is tab-separated and contains sequence names in the first and aligned sequences in the second column. Then the following code should do the job: library(msa) rawData <- read.tabl ...
written 6 months ago by ulrich.bodenhofer20
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Answer: A: What is the '?' in the result of R package 'msa' function 'msa'?
... By default, the `print()` function implemented in the '`msa`' package uses the `consensusString()` function from the '`Biostrings`' package. So please be referred to the documentation of the '`Biostrings`' package for more information on how consensus strings are computed. In any case, I guess '`?`' ...
written 6 months ago by ulrich.bodenhofer20
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Comment: C: Multiple Sequence Alignment using DNA sequence
... The 'msa' package can handle nucleotide sequences as well. This holds true for ClustalW and MUSCLE, but not for ClustalOmega (which is limited to amino acid sequences). ...
written 11 months ago by ulrich.bodenhofer20
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Answer: A: Package for custom visualization of multiple sequence alignment
... I do not know of a special R package. However, the 'msa' package's msaPrettyPrint() function provides access to all functionality of the TeXshade package via the 'furtherCode' argument. See the package vignette for a basic example (cf. p. 37). I hope that helps. ...
written 12 months ago by ulrich.bodenhofer20

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