Converting *.con.tre into Newick format

Question

[jee-wee]

Hi,

To infer duplication events on a gene tree given a species tree I'm using the Archaeopteryx package from Christian Zmasek. I would like to use a .con.tre generated by MrBayes as a gene tree. Can someone explain to me how to convert this .con.tre file into Newick format? (Without losing the posterior probability scores)

This is how the file looks like: con.tre.file

[Naren]

how does this .con.tre look like? Add the text in question.

[Michael]

This output format should be in Nexus format. Searching Nexus to Newick should help you find the answer. Nexus format should contain the tree already in Newick format in a section, so in principle it would be just copy-paste.

[jee-wee]

This is the *.con.tre file and there is no newick section present in this file. But thanks for your answer.

[arthur200126]

The part following con_all_compat IS the newick section. Remove the stuff in square brackets and you get a plain newick file. It might be fine if you don't remove it too.

[krinsman]

You're right, Archaeopteryx opened the .con.tre file as is, no problems whatsoever! Moreover, if after opening the .con.tre file in Archaeopteryx, one clicks on the "View" the menu, and then the "as Newick" option, it converts the file to Newick for the user! And then clicking "Copy to Clipboard" allowed me to paste the Newick string into a blank document really easily and get it converted to Newick. Thank you for your help!

[Michael]

Try to use FigTree to open and save as Newick like described here: how to convert a NEXUS treefile to a Newick ultrametric treefile

Answer 1

[shiy05]

Using TreeGraph2:

open nexus file with TreeGraph2, then: File - Export to tree format,

In the dialog box, choose format "newick", and choose "internal node names" : Hidden branch data with the ID "prob(percent)"

click export