[EMBOSS] Tree building
Stephen Taylor
stephen.taylor at imm.ox.ac.uk
Thu Jul 23 11:07:36 EDT 2009
Hi Frank,
> Hi Stephen,
>
>> However, I kind of need it today:-). I guess I'll have to truncate
>> them
>> to something sensible for the time being...
>
> If you need a tree *today*... :-) you could download our TOPALi
> package (loads all formats of alignment)
>
I have already installed Topali and was waiting for the results to
run. I have Over 1600 sequences and I wasn't sure when it was going to
finish since I started it this morning (using the Quick NJ option on a
Mac Mini). I think we should install it on a more powerful machine;-).
However, after I got your email I checked the status and the job had
finished. Good timing...
> It does basic NJ, but also model-selection, PhyML, RaxML and
> MrBayes. RaxML is quite fast.
>
> We internally rename species names when TOPALi submits jobs to the
> above external programs, but put the names back when we show the
> alignment and the tree.
Yes, all the labels are there in full. Thanks a lot.
Peter - I can send you some date offline if you wish.
Steve
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