Re: Morphoj map onto phylogeny

morphmet_moderator Sat, 08 Mar 2014 01:11:28 -0800

----- Forwarded message from [email protected] -----

Date: Wed, 05 Feb 2014 22:33:13 -0800
From: [email protected]
Reply-To: [email protected]
Subject: Re: Morphoj map onto phylogeny
To: [email protected]

----- Forwarded message from "Gemmell, Michael" <[email protected]> -----

Date: Sat, 1 Feb 2014 03:24:48 -0500
From: "Gemmell, Michael" <[email protected]>
Reply-To: "Gemmell, Michael" <[email protected]>
Subject: Re: Morphoj map onto phylogeny
To: "[email protected]" <[email protected]>

Hi Emma

I’m at a conference at the moment. When I get back in a week I will give things a try and let you know how it went

Thanks for getting back to me

MIke

On 1/02/2014, at 5:27 pm, <[email protected]> <[email protected]> wrote:

----- Forwarded message from Emma Sherratt <[email protected]> -----

Date: Fri, 17 Jan 2014 09:13:11 -0500
From: Emma Sherratt <[email protected]>
Reply-To: Emma Sherratt <[email protected]>
Subject: Re: Morphoj map onto phylogeny
To: Morphmet <[email protected]>
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
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Emma Sherratt, PhD.
www.emmasherratt.com
On 16 January 2014 18:17, <[email protected]> wrote:

----- Forwarded message from "Gemmell, Michael" <[email protected]> -----

Date: Wed, 15 Jan 2014 19:57:30 -0500
From: "Gemmell, Michael" <[email protected]>
Reply-To: "Gemmell, Michael" <[email protected]>
Subject: Morphoj map onto phylogeny
To: "[email protected]" <[email protected]>

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

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Re: Morphoj map onto phylogeny

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