Martin:

OK.
I'm not as familiar with the alignment tools output in R.
Your idea sounds good to me.
I would be interested in what you come up with.

Currently, we read the text file of paired alignments as a fasta file in Jalview or MacVector.
In principle we could use these programs to generate a pretty output for print, but we have not done this.
We have a large set of paired alignments (>10,000), so it makes sense to do the alignments in R first.

That's it for now,
Best,
Charles




On 4/16/12 7:06 AM, "Martin Preusse" <martin.preusse@googlemail.com> wrote:

Hi Charles,

thanks! Your solution allows to print the two alignment strings separately.

I was thinking of an output as generated by alignment tools:

AGT-TCTAT
| | | |  |  | | | |
AGTATCTAT

For this I would have to write a function to output the strings in blocks of e.g. 60 nucleotides, right?

Cheers
Martin



Am Freitag, 13. April 2012 um 19:21 schrieb Chu, Charles:

> write.XStringSet







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