Newick tree tip label was not expected about clonalframeml

[xavierdidelot]

Hello,

Yes you can use mauve to generate your input alignment, but you need to extract the core from it, ie the regions that are shared by all genomes. There is a tool to extract the core from an alignment, and it is
called stripsubsetLCBs.
You can download it for linux here:
http://darlinglab.org/mauve/snapshots/2015/2015-01-09/linux-x64/stripSubsetLCBs.bz2
Or for mac here:
http://darlinglab.org/mauve/snapshots/2015/2015-01-12/MacOS/stripSubsetLCBs.bz2
Or for windows here:
http://darlinglab.org/mauve/snapshots/2015/2015-02-26/windows/stripSubsetLCBs.exe

Best wishes,
Xavier

[pjoncour]

Hello Xavier,

Thank you very much for your fast answer. I tried many things and I still have the error.
I relaunch Mauve, extracted the core alignement (with a dedicated R script, because I couldn't make stripSubsetLCBs work). I tried with the xmfa and the fasta format.

Read 12 sequences of length 18368773 sites from ClonalFrame_Lp_genomes/Mauve_top_low_coreRG_12seq.fasta
ERROR: convert_NewickTree_to_marginal_tree(): Newick tree tip label seq9 was not expected

A managed to make ClonalFrameML worked with the input files from issue #5. But not with my files ...

Do you think you can have a look to my input files ? (Extraction of 1 block attached)
Input_block2.txt
input_tree.txt

Thank you
Best regards,
Pauline

[xavierdidelot]

Dear Pauline,

ClonalFrameML works on these two files on my computer. I think you might be using an older version of ClonalFrameML, which did not support dos formatted line endings. You could try with this alignment file, in which I converted the line endings to unix format:
converted.txt
The best solution would be to update your ClonalFrameML to the latest version.

Best wishes,
Xavier

[pjoncour]

Dear Xavier,

Thank you very much for your time !
That's great ! With your file it worked also for me. I'm using ClonalFrameML version 1.25. I'll see if I can update it or I'll convert the line endings of my files.

Thank you !

Best wishes,

Pauline