[phylocom-user] Problem Generating Family level phylogeny

Cam Webb cwebb at oeb.harvard.edu
Tue Apr 22 23:07:25 PDT 2014


Hi Ana,

There’s an inconvient ‘bug’ in the online version of phylomatic which I
haven’t had time to fix - it doesn’t like it when a terminal taxon in your
list is an internal name in the megatree (there’s a note about this on
the interface page). The solution is to make a dummy terminal in the
input list:

 facaceae/fabaceae_dummy

then make the tree and use an editor to strip out `_dummy`. 

Best,

Cam


> Ana Aldana wrote on 2014-04-23:
> 
> Hello All, 
>
> I have a list of 88 plant families for which I wish to create a
> phylogeny. But either using the online version of phylomatic or the
> downloaded version, the produced phylogeny always lacks 12 families,
> most of which are very diverse families (ie. Fabaceae). When I do the
> same procedure with the list of all the genera in my dataset
> (belonging to those 88 families) the resulting phylogeny is complete.
> So I wonder if it is impossible to produce the phylogeny I want, or
> maybe I am making a mistake in the way I introduce the data.
>
> Attached are the files I have been using.
>
> Thank you all for your time and help!
>
> Regards, 
>
> Ana M. Aldana
>
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