Here we only describe the parameters adjustable via the ARB interface.
Weighting mask
-
Specify a weighting mask for the alignment. This increases penalty for
mismatches in conservative regions and decreases it in variable regions of
the alignment.
-
Since RAxML only accepts natural numbers as weights, ARB has to multiply
the weights of e.g. POS_VAR_BY_PARSIMONY, such that the smallest weight
equals 1.
-
As a consequence the likelyhood of the calculated tree is ~ 100000 times higher
than w/o weighting mask.
Base tree / Use as constraint tree / Generate random starting tree
Nucleotide Substitution Model / Rate Distribution Model / AA Substitution Model
Please refer to the original documentation for details on Substitution Models
Number of rate categories (DNA GTRCAT only)
This option allows you to specify the number of distinct rate categories,
into which the individually optimized rates for each individual site are ?thrown?
(Default = 25)
Optimize branches/parameters
Specifies that RAxML shall optimize branches and model parameters on
bootstrapped trees as well as print out the optimized likelihood. Note,
that this option only makes sense when used with the GTRMIX or
GTRGAMMA models (or the respective AA models)!
RAxML algorithm
-
new rapid hill climbing
RAxML will execute the new (as of version 2.2.1) and significantly
faster rapid hill-climbing algorithm
-
old hill climbing
RAxML will execute the slower old search algorithm of version 2.1.3,
this is essentially just for backward compatibility.
-
optimize input tree
RAxML will optimize the model parameters and branch lengths of the
selected 'Base tree' under GTRGAMMA
-
rapid bootstrap analysis
-
tell RAxML to conduct a rapid Bootstrap analysis and search for the
best-scoring ML tree in one single program run.
-
Uses the seed specified at 'Random seed'
-
advanced bootstrap + refinement of BS tree
performs a really thorough standard bootstrap. RAxML will refine the
final BS tree under GAMMA and a more exhaustive algorithm.
-
add new sequences to input tree (MP)
-
performs just pure stepwise MP addition of new sequences
to an incomplete starting tree.
-
You have to mark all species in tree AND all species which should be
added to the tree.
-
Note: RAxML has a bug in the tree-reader and rejects many
trees as unrooted/multifurcated.
You can to use 'Tree/Beautify Tree' and select the lowest
mode (short branches first) as a workaround.
-
randomized tree searches (fixed start tree)
will perform several randomized tree searches (as specified at
'Number of runs'), that always start from one fixed starting tree.
Random seed
Used as random seed for 'rapid bootstrap analysis'
Initial rearrangement setting
-
This allows you to specify an initial rearrangement setting for the initial
phase of the search algorithm. If you specify e.g. 10 the pruned subtrees will
be inserted up to a distance of 10 nodes away from their original pruning point.
-
If you don’t specify anything here, a "good" initial rearrangement setting
will automatically be determined by RAxML.
Number of runs
Enter a number > 1 to run the selected algorithm multiple times.
Specifying e.g. '10' will result in 10 generated trees.
Select ## best trees
-
If 'Number of runs' is > 1, this specifies how many of the generated tree
shall be imported or merge using consense.
-
The trees with the best likelyhood will be selected.
What to do with selected trees?
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