Hi. After SEVERAL days running a ML optimization for a dataset of almost 300 seqs (978 nt in lenght each one), I saved an unformated file containing all the obtained data and the LF parameter table file (actually guessing that the computer was prompt to crash soon). I decided to run a BF analysis to detect selection per site and the computer crashed. SAfter rebooting I can not find a batch file that the one should be created to store of the data but the file I saved (a .nex file, I think) contains the alignment, the hyphy parameters values (TNTS, DNDS, etc), a set of calculations with the parameter values, a set of part freqs, the model and inferred tree, and the nS, S, estimates for LF values per node/seq. Question:
Is there any way to instruct hyphy to take all of this info and continue with the BF analysis to detect positive selection per site OR SHOULD I OPTIMIZE the LF function AGAIN ????. Thanks a lot for your kind reply, best wishes, Mauricio.

Sergei wrote on Mar 10^th, 2008 at 9:20am:




Hi Sergei, thanks for your reply. I have the info on a text file. I did not saved a batch file. I just want to restore the likelihood function in order to proceed to bayes analysis of site-specific selection pressure. I also saved the LF table in another file. How can I get hyphy recognize this info in order to continue with the analysis I am pursuing ?, Thanks in advance for your help, Mauricio.

PS. Before the LF table (jn the unformatted file I saved) I can see a paragraph like the following (below). Is this the Hyphy block you mentioned ?

BEGIN HYPHY;

global hyphy020808_part_Shared_TVTS=0.6094225199767913;
global hyphy020808_part_Shared_DNDS=0.179713759469559;
global hyphy020808_part_Shape_alpha=1.483316398298839;
hyphy020808_part_Shape_alpha:>0.01;
hyphy020808_part_Shape_alpha:<100;
global hyphy020808_part_Shape_beta=1.053340295516984;
hyphy020808_part_Shape_beta:>0.01;
hyphy020808_part_Shape_beta:<100;
global hyphy020808_part_Shape_beta_Inv=0.1975734488259793;
hyphy020808_part_Shape_beta_Inv:<0.9999999999;
hyphy020808_part_Categ_alpha.weights={
{              0.25}
{              0.25}
{              0.25}
{              0.25}

Hi Sergei, did you recive my email ?.  I am sorry if I insist, perhaps to run the analysis again would have taken shorter than asking about recovery of data. Thanks in advance for your reply, regards, Mauricio.