# Distance computation algorithms

**URL:** <https://forum.mothur.org/t/distance-computation-algorithms/60>\
**Category:** Commands in mothur\
**Created:** [November 29, 2009, 7:47pm UTC](https://forum.mothur.org/t/distance-computation-algorithms/60 "2009-11-29T19:47:58Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![jamesafoster](https://avatars.discourse-cdn.com/v4/letter/j/a9a28c/32.png) [@jamesafoster](https://forum.mothur.org/u/jamesafoster)\
**Post date:** [November 29, 2009, 7:47pm UTC](https://forum.mothur.org/t/distance-computation-algorithms/60/1 "2009-11-29T19:47:58Z")

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What algorithm(s) are used to compute distance matrices?

I understand the options in the dist.seqs command, but I’d like to know more about the algorithms used.

With DNADIST, for example, I can use different correction models (FK84, JC, etc.). Is there such an option in mothur?

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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 1, 2009, 8:44pm UTC](https://forum.mothur.org/t/distance-computation-algorithms/60/2 "2009-12-01T20:44:32Z")

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So we don’t currently include support for the models of multiple substitutions like JC, etc. Part of the reason is that those models ignore gaps. The algorithms in mothur either ignore gaps, count a string of gaps as a single insertion/deletion, or count each gap as an insertion/deletion. Whether to ignore gaps or not can clearly have a significant impact on the distances. We’ll add this to the “list” of future features…

Pat