RAxML BlackBox
Constraint specification
This option allows you to specify an incomplete or comprehensive multifurcating constraint tree for the RAxML search in NEWICK format. Initially, multifurcations are resolved randomly. If the tree is incomplete (does not contain all taxa) the remaining taxa are added by using the MP criterion. Once a comprehensive (containing all taxa) bifurcating tree is computed, it is further optimized under ML respecting the given constraints.
Important: If you specify a non-comprehensive constraint, e.g., a constraint tree that does not contain all taxa, RAxML will assume that the remaining taxa, that are not contained in the constraint topology are unconstrained, i.e., these taxa can be placed in any part of the tree.
As an example consider an alignment with 10 taxa: Loach, Chicken, Human, Cow, Mouse, Whale, Seal, Carp, Rat, Frog .
If for example you would like Loach, Chicken, Human, Cow to be monophyletic you would specify the constraint tree as follows:
((Loach, Chicken, Human, Cow),(Mouse, Whale, Seal, Carp, Rat, Frog));
Moreover, if you would like Loach, Chicken, Human, Cow to be monophyletic and in addition Human, Cow to be monophyletic within that clade you could specify:
((Loach, Chicken, (Human, Cow)),(Mouse, Whale, Seal, Carp, Rat, Frog));
If you specify an incomplete constraint:
((Loach, Chicken, Human, Cow),(Mouse, Whale, Seal, Carp));
the two groups Loach, Chicken, Human, Cow and Mouse, Whale, Seal, Carp will be monophyletic, while Rat and Frog can end up anywhere in the tree.
Binary backbone specification
This option allows you to pass a binary/bifurcating constraint/backbone tree in NEWICK format to RAxML. Note, that using this option only makes sense if this tree contains less taxa than the input alignment. The remaining taxa will initially be added by using the MP criterion. Once a comprehensive tree with all taxa has been obtained it will be optimized under ML respecting the restrictions of the constraint tree.

When publishing results obtained via the web-server please cite:
A. Stamatakis, P. Hoover, J. Rougemont
A Rapid Bootstrap Algorithm for the RAxML Web-Servers,
Systematic Biology, 75(5): 758-771, 2008