Comments (4)
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
from clonalframeml.
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
from clonalframeml.
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
from clonalframeml.
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
from clonalframeml.
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from clonalframeml.