[Primeusers] Release 1.0 of PrimeGSR

[Lars Arvestad]

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)??


-- 
School of Computer Science and Communication
and Stockholm Bioinformatics Center
http://www.csc.kth.se/~arve