Output explanations

[ConstantinV]

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.

[shlomobl]

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!

[shlomobl]

Hi again,
What are the numbers in the CGAV tree? How to read them in terms of significance?
Are there bootstrap values?

[ConstantinV]

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.

[shlomobl]

Thanks, but I can't find it in the site. Do you have the specific ref.?

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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. — Reply to this email directly, view it on GitHub <#23 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABKL3XPBJ33L6ZS5774BLRLVVUM6XANCNFSM54BBPZ4Q> . You are receiving this because you commented.Message ID: ***@***.***>