unordered, ordered? Fitch, Wagner?

[Deneb García Avila]

Dear All,

Can somebody tell me which are the default settings in POY for the
following issues?

1) Is POY treating molecular characters under Direct Optimization as unordered?
2) How POY contabilizes steps when differencial step matrices are
applied (e.g. 1:1:2, 1:4:4) ? I mean, is POY counting each step
transformation (in either direction) as one step transformation if
yes, can it be considered as "equivalent" to Fitch parsimony?

Thanks a lot in advance!

Regards,
Deneb

--
Deneb García-Avila
Km 2.5 carretera antigua a Coatepec 351
Depto. Biodiversidad y Sistemática
Instituto de Ecología, AC
91070 Xalapa, Veracruz
México

Tel: 52(228) 842-1800 ext 3105, 3010
email: dene...@gmail.com, deneb....@posgrado.inecol.edu.mx

[Andres Varon]

Hello Deneb,

On Apr 21, 8:36 pm, "Deneb García Avila" <deneb...@gmail.com> wrote:
> Dear All,
>
> Can somebody tell me which are the default settings in POY for the
> following issues?
>
> 1) Is POY treating molecular characters under Direct Optimization as unordered?

Depends on the cost matrix you choose. The default cost matrix assigns
cost 1 to every substitution, and 2 to every indel, which is, strictly
speaking, not an unordered character.

> 2) How POY contabilizes steps when differencial step matrices are
> applied (e.g. 1:1:2, 1:4:4) ? I mean, is POY counting each step
> transformation (in either direction) as one step transformation if
> yes, can it be considered as "equivalent" to Fitch parsimony?

No. We count as many steps as the matrix says. If the matrix says A ->
C is 2, then 2 steps are counted when A and C are aligned over a
branch of the tree.

I am not sure if I am understanding the question ...

Sorry for the delay to respond, I'm catching up with a large chunk of
emails that are now queued on my mailbox.

best,

Andres

>
> Thanks a lot in advance!
>
> Regards,
> Deneb
>
> --
> Deneb García-Avila
> Km 2.5 carretera antigua a Coatepec 351
> Depto. Biodiversidad y Sistemática
> Instituto de Ecología, AC
> 91070 Xalapa, Veracruz
> México
>
> Tel: 52(228) 842-1800 ext 3105, 3010

> email: deneb...@gmail.com, deneb.gar...@posgrado.inecol.edu.mx

[Deneb García Avila]

Thank you Andres!
Do not worry about the delay :)

All the best,
Deneb

2008/5/8 Andres Varon <ava...@gmail.com>:

email: dene...@gmail.com, deneb....@posgrado.inecol.edu.mx