Question: Which ete3 format to parse a newick file with concordance values?
0
gravatar for mrmrwinter
5 months ago by
mrmrwinter30
University of Hull
mrmrwinter30 wrote:

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

ADD COMMENTlink written 5 months ago by mrmrwinter30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1279 users visited in the last hour
_