search

Pas-Kapli / mptp

mPTP - a tool for single-locus species delimitation
GNU Affero General Public License v3.0
25 stars 5 forks source link

Support taxon names like 'my_taxon' #66

Closed lutteropp closed 8 years ago

lutteropp commented 8 years ago

If a tree contains taxon names enclosed in ', mptp simply outputs "Tree is neither unrooted nor rooted. Go fix your tree."

The same happens with the use of the character "|" in taxa names.

If we don't fix this in the tree parser, I expect that many users will ask annoying questions about what is wrong with their tree. And it will not even be the user's fault because we never say anywhere which characters are allowed in taxa names.

stamatak commented 8 years ago

yes, that should be fixed ...

alexis

On 10.04.2016 12:51, Sarah Lutteropp wrote:

If a tree contains taxon names enclosed in ', mptp simply outputs "Tree is neither unrooted nor rooted. Go fix your tree."

If we don't fix this in the tree parser, I expect that many users will ask annoying questions about what is wrong with their tree.

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/Pas-Kapli/mptp/issues/66

Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University of Arizona at Tucson

www.exelixis-lab.org

stamatak commented 8 years ago

you may also want to add a check that assesses if the input tree is ultrametric, since this is something we actually don't want for PTP,

alexis

On 10.04.2016 12:51, Sarah Lutteropp wrote:

If a tree contains taxon names enclosed in ', mptp simply outputs "Tree is neither unrooted nor rooted. Go fix your tree."

If we don't fix this in the tree parser, I expect that many users will ask annoying questions about what is wrong with their tree.

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/Pas-Kapli/mptp/issues/66

Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University of Arizona at Tucson

www.exelixis-lab.org

xflouris commented 8 years ago

done