The random seed is set to guarantee that you will generate a
deterministic parsimony starting tree. Thus we have reproducible runs,
since different seeds will generate different starting trees which in
turn will lead to different ML trees (but given a seed, you always get
the same final ML tree).
In general you should use a random number as a starting seed.
May the force be with you,
Fernando
Please note that the scope of this group should cover only
raxml-related questions.
For background questions on computational phylogenetics such as
bootstraping you can have a look at Ziheng Yang's textbook
"computational molecular evolution" or Felsenstein's "Inferring
Phylogenies".
Best,
Fernando
the procedure/algorithm that is used is called randomized stepwise addition order and described in the RAxML-III paper
from 2005
Alexis
--
Dr. Alexandros Stamatakis
www.exelixis-lab.org
Trees explored better will be...
This is an interesting question. However, it is difficult to know what
is a good starting tree. According to our experience, trees that start
not being promising in terms of LH may take search paths that end up
leading to the better ML trees. In other words, we are not aware of
any straight forward way to identify "good starting trees" early in
the search phase.
As far as I know, the closest we have done to that is limiting tree
search to a inner part of the tree, which is faster than the search on
the full trees. We saw there that the good starting trees for the
constraint search (SPR moves only in the inner part of the tree) where
also good trees when the full search (SPRs on the full tree) was done.
The later has been discussed here:
F. Izquierdo-Carrasco, S.A. Smith, A. Stamatakis: "Algorithms, Data
Structures, and Numerics for Likelihood-based Phylogenetic Inference
of Huge Trees". BMC Bioinformatics 12:470 2011
Cheers,
Fernando
If you want to experiment with this idea, get the latest Parsimonator version from github that now reports parsimony
scores and generate say 1000 starting trees and then extract the 10 best ones or so.
But as Fernando says, search space is weird and a good starting tree in terms of parsimony score will not necessarily
generate a good ML tree.
Alexis
--
Dr. Alexandros Stamatakis
www.exelixis-lab.org