Dear all

[Emanuelle Corrêa]

Dear all,

I am working with some aminoacids and I was thinking about the cost matrix called with the command tcm. I am using tcm11, tcm1,2 tcm1,3 and so on changing the cost of indels compared to substitutions, with the intention to perform a sensitivity analysis. Is there any possibility that the program is understanding an indel only for changes (insertions and deletions) involving A, C, G, T?Now, taking a look at the topologies, what are the options, since I have only one set of data, to choose one of the topologies?                                                                               

I am still waiting for some clue on how to construct and use a different cost matrix for aminoacids in which different substitutions receive different costs.

Thanks to all

lely                                                                                                                                                                                                                                                                                                                                 

[Andres Varon]

Hello Emmanuelle,

On May 9, 2008, at 9:13 AM, Emanuelle Corrêa wrote:

> Dear all,
> I am working with some aminoacids and I was thinking about the cost
> matrix called with the command tcm. I am using tcm11, tcm1,2 tcm1,3
> and so on changing the cost of indels compared to substitutions,
> with the intention to perform a sensitivity analysis. Is there any
> possibility that the program is understanding an indel only for
> changes (insertions and deletions) involving A, C, G, T?Now, taking
> a look at the topologies, what are the options, since I have only
> one set of data, to choose one of the topologies?
> I am still waiting for some clue on how to construct and use a
> different cost matrix for aminoacids in which different
> substitutions receive different costs.

Follow the same format as in the example of tcm in page 110 of the
manual, but for the aminoacid alphabet in the following order (for
columns and rows):

alanine
arginine
asparagine
aspartic
cysteine
glutamine
glutamic
glycine
histidine
isoleucine
leucine
lysine
methionine
phenylalanine
proline
serine
threonine
tryptophan
tyrosine
valine
gap

We should add that information to the manual.

best,

Andres

> Thanks to all
> lely
>
> >