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PoonLab / Kaphi

Kernel-embedded ABC-SMC for phylodynamic inference
GNU Affero General Public License v3.0
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R cannot read Newick tree file returned from MASTER #109

Closed gtng92 closed 6 years ago

gtng92 commented 6 years ago

Error message:

The tree has apparently singleton node(s): cannot read tree file.
  Reading Newick file aborted at tree no. 1

Newicks can be read with FigTree but not by R. The response to this error thrown is found here which suggests using function clean.phylo in Phylocom.

ArtPoon commented 6 years ago

You can tell MASTER to collapse singleton nodes when outputting the newick file, the argument is collapseSingleChildNodes="true"

On Sep 12, 2017, at 2:40 PM, Tammy Ng notifications@github.com wrote:

Error message:

The tree has apparently singleton node(s): cannot read tree file .

Reading Newick file aborted at tree no. 1 Newicks can be read with FigTree but not by R. The response to this error thrown is found here which suggests using function clean.phylo in Phylocom.

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gtng92 commented 6 years ago

Oh ok thank you!