PEPPAN
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zheminzhou
Output explanations
Hello, thank you for great tool! I wonder what mean the output locus tag names in *.PEPPAN.gene_content.Rtab file for example LBv2v5_001134/12 -The LBv2v5_001134 is a locus tag name but the following postfixes for locus tags (/12 or /0.1 or /2/0.1) I can not clearly understand. 2) Is there any scripts to extract concatenated core alignment from result files?
Thank you in advance.
Hello, I second that :-) 1- Is there a way to output the matrix the other way around: lines = genomes, columns = genes? This seem to be the format for grapetree and phyloviz. 2- I was hoping to be able to extract the concatenated core seqs. too (like in Roary and similar tools)! I will add another one, please: 3- Is there a way to extract the alignments of specific genes? Thanks!
Hi again, What are the numbers in the CGAV tree? How to read them in terms of significance? Are there bootstrap values?
Hi again, What are the numbers in the CGAV tree? How to read them in terms of significance? Are there bootstrap values? I suppose CGAV tree build by MSTreeV2 based on PEPPAN.CDS_CGAV.profile file. See https://enterobase.readthedocs.io/en/latest/grapetree/grapetree-about.html for details. I do not think that it has bootstrap values.
Thanks, but I can't find it in the site. Do you have the specific ref.?
On Sun, Jul 24, 2022, 13:43 ConstantinV @.***> wrote:
Hi again, What are the numbers in the CGAV tree? How to read them in terms of significance? Are there bootstrap values? I suppose CGAV tree build by MSTreeV2 based on PEPPAN.CDS_CGAV.profile file. See https://enterobase.readthedocs.io/en/latest/grapetree/grapetree-about.html for details. I do not think that it has bootstrap values.
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