I’m sorry if the question has been asked already, I couldn’t find my answer in this forum, nor on Google.
Is there a any way to use a custom score matrix for aligning sequences in mothur?
Where in the code base could I plug that? I had a quick look at it, but couldn’t figure it out myself.
For those curious of why I want to be able to do that: I have millions of reads that I want to align on a few reference sequences. Those reads come from bisulfite converted sequencings, and I want to be able to align sequences by context priority: 1) GxG (to get the maximum of CG or TG on top of each other), then 2) CxC & CxT & TxT (same reason), and then 3) the rest of the bases.
Thank you very much in advance, and have a nice day!