# Custom score matrix

**URL:** <https://forum.mothur.org/t/custom-score-matrix/19627>\
**Category:** Feature requests\
**Created:** [December 5, 2018, 3:55pm UTC](https://forum.mothur.org/t/custom-score-matrix/19627 "2018-12-05T15:55:24Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Marc\_M](https://avatars.discourse-cdn.com/v4/letter/m/35a633/32.png) [@Marc\_M](https://forum.mothur.org/u/Marc_M)\
**Post date:** [December 5, 2018, 3:55pm UTC](https://forum.mothur.org/t/custom-score-matrix/19627/1 "2018-12-05T15:55:24Z")

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Hello,

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!  
Marc

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**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [December 7, 2018, 12:02pm UTC](https://forum.mothur.org/t/custom-score-matrix/19627/2 "2018-12-07T12:02:47Z")

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

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**Author:** ![Marc\_M](https://avatars.discourse-cdn.com/v4/letter/m/35a633/32.png) [@Marc\_M](https://forum.mothur.org/u/Marc_M)\
**Post date:** [December 7, 2018, 2:02pm UTC](https://forum.mothur.org/t/custom-score-matrix/19627/3 "2018-12-07T14:02:06Z")

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Hi,

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

Thanks!  
Marc

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**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [December 10, 2018, 6:59pm UTC](https://forum.mothur.org/t/custom-score-matrix/19627/4 "2018-12-10T18:59:41Z")

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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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**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\
**Post date:** [December 20, 2018, 6:59pm UTC](https://forum.mothur.org/t/custom-score-matrix/19627/5 "2018-12-20T18:59:44Z")

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