GARLI-IUPAC CODE?

[Natalia Trujillo Arias]

Hi all,

Could anyone tell me how Garli deals with site polymorphisms (i.e. those sites coded using the IUPAC 'ambiguity' codes)?

is there any option that I will have to modified into the input (garli.conf) to garli recognize the iupac code?

thanks!

[Adam Bazinet]

Not that I'm aware of, but Derrick can confirm.

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[Derrick Zwickl]

Hi Natalia,

Adam's right, there's nothing you need to do to get it to correctly interpret IUPAC codes.  As for how the ambiguity codes are dealt with, they are treated as partial ambiguity, as with PAUP, MrBayes and other programs.  So, a site that is an R takes into account the likelihood of it being an A and of it being a G.

Best,
Derrick

[Natalia Trujillo Arias]

Thanks!

El viernes, 20 de febrero de 2015, 20:23:33 (UTC-3), Adam Bazinet escribió:

Not that I'm aware of, but Derrick can confirm.

On Friday, February 20, 2015, Natalia Trujillo Arias <natitr...@gmail.com> wrote:

Hi all,

Could anyone tell me how Garli deals with site polymorphisms (i.e. those sites coded using the IUPAC 'ambiguity' codes)?

is there any option that I will have to modified into the input (garli.conf) to garli recognize the iupac code?

thanks!

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