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 results. Please help me to do the same.

Many thanks in advance.

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.

  • $\begingroup$ 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. $\endgroup$
    – M__
    Mar 21, 2022 at 12:36
  • $\begingroup$ 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). $\endgroup$
    – gringer
    Mar 21, 2022 at 21:36


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