Question: Tuning MrBayes - Swapfreq, Nswaps, Nchains, and Temp
0
gravatar for gykajan
4 months ago by
gykajan0
gykajan0 wrote:

Hi,

For an alignment containing 1000s of sequences, what is the best setting for Swapfreq, Nswaps, Nchains, and Temp in MrBayes? I am running an MPI version and tried to raise the number of chains (Nchains) each running on a different CPU core. But did not get significant time decrease compared to 8 chains on 8 cores. Convergence diagnostics and automatic stopping was ON (stoprule=yes stopval=0.01).

Thx,
Victor

ADD COMMENTlink modified 4 months ago by RamRS20k • written 4 months ago by gykajan0

See What do I do when it is difficult to get convergence.

ADD REPLYlink written 4 months ago by h.mon22k

Thanks for the tip, checked it out. It just seems impractical. You have your large dataset, the analysis converges, but takes ages. If it is done already, you don't start to optimise it. Is there any way/hint to set up these values correctly for a large number of chains/cores?

ADD REPLYlink written 4 months ago by gykajan0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1457 users visited in the last hour