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zheminzhou / PEPPAN

Phylogeny Enhanded Prediction of PAN-genome
https://doi.org/10.1101/2020.01.03.894154
GNU General Public License v3.0
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Output explanations #23

Open ConstantinV opened 2 years ago

ConstantinV commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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

ConstantinV commented 2 years ago

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 commented 2 years ago

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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