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, possibly with gaps), then it is possible to directly convert them using AAMultipleAlignment(mySequences) or, if you want the data structures as used by the msa package: as(AAMultipleAlignment(mySequences), "MsaAAMultipleAlignment")
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.
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.
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 (bodenhoferatbioinf.jku.at) and I will try to go deeper into the problem.
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, you need to study the features of TeXshade and use the furtherCode argument of the msaPrettyPrint() function. An example is shown in Section 7.4 of the package vignette.
hm, it still doesn't work:
which result in error
...and it does work as expected on toy examples from package manual, so latex is set up properly
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.
no, sry - still this problem (also, i'm on mac, not windows)
I suggest you change
output="pdf"tooutput="tex"and runpdflatexon the resulting filenewaln.tex, and look what error message is thrown. Unfortunately, thetexi2dvi()function does not convey enough information about what the problem is.ok, here is what i got from
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 (bodenhoferatbioinf.jku.at) and I will try to go deeper into the problem.
also can you help me with dna alignments? If i'm willing to realign with, for example muscle, i do it this way:
and in my output i got this:
Can i color only matching letters on a DNA, or is this package for AA only? link for image doesn't work, so here is it https://imgur.com/JG2NjUF
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 thatNis treated like a regular character, my suggestion is simple: replace allN's with dashes. If you need more custom functionality, you need to study the features of TeXshade and use thefurtherCodeargument of themsaPrettyPrint()function. An example is shown in Section 7.4 of the package vignette.