Re: [Dart-help] help with windowlicker

[marcin j. <mar...@gm...>]

much better, thanks!
I did notice the trees for each alignment in the output ...

The tree estimation is running, I'll keep reporting ...


On Thu, Apr 24, 2008 at 7:22 PM, Ian Holmes <ih...@be...> wrote:
> 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.
>