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Pas-Kapli / mptp

mPTP - a tool for single-locus species delimitation
GNU Affero General Public License v3.0
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Tree is neither unrooted nor rooted #81

Open Onaalvarez opened 6 years ago

Onaalvarez commented 6 years ago

Hi everyone,

I have a problem when I want to run mPTP with my data. Although my tree is rooted and I have an outgroup, the pipe is broken and this message appears: "Tree is neither unrooted nor rooted". Could there be a limit on the number of Taxa that act as an outgroup? In my case I am including 17 ... are they too many? Anyway, I tried to run the program also without the --outgroup option and it gives to me the same error.

Thank you

Marta

Pas-Kapli commented 6 years ago

Hi Marta,

there is no limit on the number of outgroup taxa. This error message is a bit misleading, sorry about that, it comes up with any format problem there might be in your tree file. For example, it could be that your tree has some multifurcations or some annotations (e.g. figtree annotations). If you cannot identify the problem, I can take a look if you send it to me (k.pashalia@gmail.com).

Best, Paschalia

Onaalvarez commented 6 years ago

Thank you for your quick answer. Finally I could solve it. I detected (as you said) some annotations from figtree.

Cheers

Marta

Spookpadda commented 6 years ago

Hi, We are struggling with the "Tree is neither unrooted nor rooted" issue. Our Newick file is binary (all interior nodes give rise to two daughters) but there are many zero branch lengths. Is that a problem?

stamatak commented 6 years ago

please send me the tree to my personal email address and re-post your issue on the ptp google group. We will reply there.

Alonso-Garcia commented 4 years ago

Hello everyone, I'm also having problems to run my IB tree from MrBayes in my server. I have exported the tree in newick format from FigTree, both rooting (midpoing) and without rooting the tree. I have always the same error:

Tree is neither unrooted nor rooted.
mptp 0.2.4_linux_x86_64, 882GB RAM, 64 cores
https://github.com/Pas-Kapli/mptp

Parsing tree file...

I run a ML tree from RAxML in mPTP and it worked.

Please, could you help me to figure it out? Thank you,

Marta

xflouris commented 4 years ago

Hi @Alonso-Garcia ,

Could it be your tree does have some annotation (e.g. support values)? If that's the case you need to remove it and have only a tree with branch lengths. Otherwise, can you send the tree to my personal email: flouris at gmail dot com

best, tomas

Alonso-Garcia commented 4 years ago

Thank you for your quick answer. I would say it hasn't but, I'll send it to you. It would be great if you could have a look at it. Cheers Marta