[Primeusers] Release 1.0 of PrimeGSR

[Filipe Garrett]

Yes, I was referring to the same tree but having the root at 0.5 instead of 1.
This tree only works in prime GSR with a "-c" option of, at least, 500 and this greatly increases 
time and memory usage. I suppose it can be because when scaling the tree some branches are just too 
small. I just thought it was strange....

By the way, is it possible to execute primeGSR in parallel (threads, pvm, mpi, ....)?
Are you planning to add a chapter to the manual to explain the MCMC output?

thanks a lot for your help and time,
FG


Lars Arvestad wrote:
> I am not sure what you mean by "branch lengths roughly half of the 
> branches of the 1.0 root tree".
> 
> Do you mean the root is at 0.5?
> 
> The number after -c affects the run time quadratically, but the actual 
> branchlengths should not affect memory.
> 
>     Lars
> 
> 
> 
> Filipe Garrett wrote:
>> Scaling the tree to 1.0 at the root apparently works (still running) with both 90 ("-c 200") and 375 
>> ("-c 400") sequences; although with 375 sequences needs too much memory (around 11Gb).
>>
>> Changing the "-c" option greatly influences memory usage and speed. I've also tried a scaled tree 
>> with branch lengths roughly half of the branches of the 1.0 root tree, and it only works with "-c" 
>> equal to at least 500. Is it normal that a reduction in branch lengths to half leads to such an 
>> increase in memory usage and time (from 700Mb to 4Gb and approx. 10x slower)??
> 
> 

-- 
Filipe G. Vieira
Departament de Genetica
Universitat de Barcelona
Av. Diagonal, 645
08028 Barcelona
SPAIN
Phone: +34 934 035 306
Fax: +34 934 034 420
fgarret at ub.edu
http://www.ub.edu/molevol/