Method used in the command dist.seqs

Commands in mothur
1

Hi,

I’d like to know what method is used in the command dist.seqs to calculate the distance matrix of a sequences dataset.

Thanks for any information,

Cheers,

Guillaume.

2

Do you need something more specific than is provided here?

http://www.mothur.org/wiki/Dist.seqs

3

Thanks you, I already read this wiki information but indeed I am still missing some informations.
I mean, what is the model of distance used (Kimura, Jukes-Cantor, LogDet,…) ? The transition/transversion ratio ? and others types of criteria which are usually possible to set in the program DNADIST.

Thanks you for your answer,

G.

4

We do not employ a correction for multiple substitutions since those models basically use the ignore gaps approach and correct the distance. Those corrections have been developed for more rapidly evolving protein coding sequences. The norm across the field has been to not correct for multiple substitutions and to treat the gaps as a mismatch.

5

Ok. Thank you very much for your assistance.