Custom score matrix


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!

I’m sorry, but at this time there isn’t - the only settings are for match/mismatches, gap openings, and gap extensions.


Thank you for your answer.
Would you happen to know if there is any way I could plug it somewhere in the code?


sorry, it’s only coded as match/mismatch - there isn’t an easy way to make it more specific than that.

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