Which ete3 format to parse a newick file with concordance values?
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12 months ago
mrmrwinter ▴ 30

Hi

I am trying to plot several trees in toytree but it is returning an error.

Unexpected newick format 100/48.8/63.1:0.0045539444

The tree was made in IQTREE using the -gcf and -scf commands to calculate and apply concordance factors as support values.

I have checked the documentation of iqtree, toytree and ete, but cant find a solution.

The actual tree file looks like this:

(MjavVW4_2:0.0037628199,((MincW1_2:0.0034335950,MfloSJF1_2:0.0025424477)100/52.8/65.8:0.0033103358,((((MentL30_2:0.0113434253, MentL30_1:0.0130780460)100/61.5/64.2:0.0050474409,Mhaplanaria_2:0.0096054956)30/0:0.0000120718,Mhaplanaria_1:0.0198643385)89/51.4/36.8:0.0007650738, (((MjavVW4_1:0.0024033931,MareHarA_1:0.0024185012)81/40/53.6:0.0012601736,MincW1_1:0.0028959664)86/33.3/28.6:0.0026290506, MfloSJF1_1:0.0042819665)100/46.2/54:0.0055878340)100/42/60.7:0.0018777500)100/45.5/52.5:0.0031768288,MareHarA_2:0.0047350710);

Many thanks

iqtree phylogenetics concordance factors newick • 382 views
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