<p>I need to know whether my <code>pan-genome</code> is <code>open or closed</code>. For that, I need to calculate the <code>Heaps Alpha value</code> from my <a href="https://sanger-pathogens.github.io/Roary/" rel="nofollow noreferrer">roary pipeline</a> results. Please help me to do the same.</p>
<p>Many thanks in advance.</p>
<hr />
<p>Directly quoting from the link provide:</p>
<p>Roary By Andrew Page based on version 3.11.2 (22-Jan-2018)</p>
<p>Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results.</p>

CC BY-SA 4.0
2022-03-21T12:36:10.457Z
I edited the question to give details of Roary. I personally find the context difficult to follow and further details would be helpful, such as the aim of the project as well as the genomes being used.
M__
CC BY-SA 4.0
2022-03-21T21:36:13.057Z
If this is a homework question (or otherwise canned question with a known answer), could you please tag as 'homework'? Also, please provide additional context around what you're trying to do (e.g. sample type, project goal).
gringer
<phylogenetics><gene><genome><phylogeny><genomics>
Help me to calculate Heaps Alpha value from the roary pangenome pipeline result?
# Help me to calculate Heaps Alpha value from the roary pangenome pipeline result?

(Asked by: username_0 on 2022-03-21)

I need to know whether my `pan-genome` is `open or closed`. For that, I need to calculate the `Heaps Alpha value` from my [roary pipeline](https://sanger-pathogens.github.io/Roary/) results. Please help me to do the same.

Many thanks in advance.

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Directly quoting from the link provide:

Roary By Andrew Page based on version 3.11.2 (22-Jan-2018)

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results.

**Tags:** phylogenetics, gene, genome, phylogeny, genomics
> **Comments:**
> **username_1**: I edited the question to give details of Roary. I personally find the context difficult to follow and further details would be helpful, such as the aim of the project as well as the genomes being used.  
> **username_2**: If this is a homework question (or otherwise canned question with a known answer), could you please tag as 'homework'? Also, please provide additional context around what you're trying to do (e.g. sample type, project goal).  

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## 0 answers

