----- Forwarded message from Emma Sherratt
<emma.sherr...@gmail.com> -----
Date: Fri, 17 Jan 2014
09:13:11 -0500
From: Emma Sherratt <emma.sherr...@gmail.com>
Reply-To: Emma Sherratt <emma.sherr...@gmail.com>
Subject:
Re: Morphoj map onto phylogeny
To: Morphmet
<morphmet@morphometrics.org>
Mike,
I have used MorphoJ and that particular
function for several years so lets see if I can be of
assistance.
The error you describe means there is a
discrepancy between the dataset and matching of the tip labels of the tree. This
shouldn't be a nexus file issue. A simple I/O issue that should get fixed if you
make sure of the following points.
1) for your morphological dataset, have a classifier called
"Phylo ID" or something suitable. The names for each taxon should match EXACTLY
the names on the tips of the tree in your nexus file.
2) Make a subset of your data to contain only species that
are in the phylogeny. If you have non-phylogeny species in there, it could cause
troubles (and I think that might be the case from your error).
3) import the nexus file, and make sure the names are what
you expected. Sometimes if they are long, or have _ or spaces things can go
skewy.
4) when in Map onto Phylogeny, make sure to
choose "Phylo ID" or whatever you called it, as the classifier to match to the
tips.
If you have further troubles, send me your morphoJ file and
I can have a look.
Emma
On 16 January 2014 18:17, <morphmet_modera...@morphometrics.org>
wrote:
----- Forwarded message from "Gemmell, Michael" <m.r.gemm...@massey.ac.nz> -----
Date: Wed, 15 Jan 2014 19:57:30 -0500
From: "Gemmell, Michael" <m.r.gemm...@massey.ac.nz>
Reply-To: "Gemmell, Michael" <m.r.gemm...@massey.ac.nz>
Subject: Morphoj map onto phylogeny
To: "morphmet@morphometrics.org" <morphmet@morphometrics.org>
Hi
I am having trouble with the map onto phylogeny function in morphoj. I am getting an error message saying "The following names are in the data set but not in the phylogeny: o c l v"
These are species classifiers extracted from the names of the samples.
I have ≈40 samples from 4 species. I guess there needs to be something in the nexus file which is missing. Has anyone mapped onto phylogeny successfully? if so would it be possible to have a look at the .nex file to see where mine differs, or if anyone had instructions to help me edit the file so morphoj can read it correctly. I made my phylogeny file using SplitsTree if that info is of any use.
Regards
Mike Gemmell
----- End forwarded message -----
----- End forwarded message
-----
