enrico wrote:
> Hi,
>> I need to compute arbitrary time PAM matrices (where time is continuous
> and not discrete). I know that this is quite easy having the
> instantaneous rate matrix (i.e. P(i,j,t) = exp(Q*t)). Unfortunatly I
> wasn't able to find such rate matrix, is there someone who can help?
>> Thanks in advance.
>> Enrico Varriale
>
A very good reference is this:
@ARTICLE{MuellerV00,
author = {Tobias M{\"u}ller and Martin Vingron},
title = {Modeling Amino Acid Replacement},
journal = JCB,
year = {2000},
volume = {7},
pages = {761--776},
number = {6},
}
JCB is Journal of Computational Biology. The rate matrix for the VT
series of matrices is provided. Not strictly PAM, though.
HTH,
Niklas
