Re: [Dart-help] help with windowlicker

[Ian H. <ih...@be...>]

marcin joachimiak wrote:
> Excellent, its working now!

Cool!

> I'll have the tree data soon and may try a run with as well, but best
> if I could know that the other tree is different from the xrate one
> with the Jukes-Cantor model. Can I get the Jukes-Cantor model
> tree/distances from xrate?

Yes, it will insert the trees into the alignment files it outputs, using
the New-Hampshire-encoded-in-Stockholm format from my previous email.

One caveat. The way you're running it now, it is calculating a separate
tree *for every window* in the alignment. This may not be what you want,
and it's certainly going to slow things down.

If you want to calculate the tree just once for the whole alignment, type

xrate MY_ALIGNMENT.stock -e $DARTDIR/grammars/jukescantor.eg
--noannotate -log 5 > MY_ALIGNMENT_WITH_TREE.stock


The "--noannotate" just means "don't waste time trying to annotate this
alignment, I just want the tree". The "-log 5" will just print some log
messages on stderr, so you can watch the progress of the tree-building
algorithms.

hth,

I.