Korbinian Strimmer strimmer at zi.biologie.uni-muenchen.de
Tue Apr 23 11:35:54 EST 1996

ProtML and NucML deal only with unrooted trees, therefore you *must* have a trichotomy
at the base of your tree. Here is an excerpt of the MOLPHY documentation:

> Note that the machine readable tree is an UNROOTED one, and therefore its base
> must be multifurcation with a multiplicity of greater than or equal to three.
>     Unrooted tree (PROTML & DISTNJ)        Rooted tree (not allowed)
>        variable rate                          constant rate
>     ( subtree1, subtree2, subtree3 );      ( subtree1, subtree2 );
>         :-----subtree1
>         :                                      :-----subtree1
>         :-----subtree2                         :
>         :                                      :-----subtree2
>         :-----subtree3
>                                                ^root
>         ^provisional root

Your tree, however, is a rooted one:


If you use a constraint tree to speed up an exhaustive search the syntax is different
from that of a normal user tree (you tree looks like a user tree). Again some words
from the docs:

>                   Format of CONSTRAINED TREE File
> 	standard CONSTRAINED TREE file format:
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Note, "~~~" is file separater.
> CONSTRAINED TREE file allow constrained machine readable tree.
> Pair of PARENTHESIS indicates FIX tree structure, but Pair of BRACE indicates
> COMBINATION tree structure in a monophyletic group.

If you look carefully you'll see that there are in addition to normal '(' brackets the
curly ones '{'.  If you want to impose a constraint tree you have to write the constraint
tree into a separate file (I call it tree.cns).

Let us now check the syntax of the command:

  protml -jf -s -v -i a.phy

You call the STARDECOMPOSITION method (-s) along with the FTT-F model. Instead, you should type   
 protml -jf -e a.phy tree.cns > output.txt
which performs an exhaustive search considering the constraint file tree.cns writing the output to

Korbinian Strimmer

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