Description of Heatmap Outputs

[jpearl01]

Summary:

I'm familiar with ANI (and there is a very good description of it in the README), so the *_percentage_identity, *_alignment_length, and *_alignment_coverage make sense to me.

I'm not so sure about the *_hadamard or *_similarity_errors graphs. Is there a good resource to find out more as to how to interpret these? Or the algorithms used to generate them?

pyani Version: pyani-0.2.1

Python Version: 3.5.0b4

Operating System: Fedora 23

[widdowquinn]

Other than the source code, I'm just going to have to explain them here ;)

The *_hadamard output is the [https://en.wikipedia.org/wiki/Hadamard_product_(matrices)](Hadamard product) of identity and coverage. It's meant to provide a measure that allows you to interpret identity and coverage simultaneously - it's not provided by any other ANI package so far as I know. It'll be a new thing for the pyani paper.

The *_similarity_errors graphs come out of using MUMmer - it's a value provided in MUMmer output that essentially counts up SNPs (but doesn't identify them directly).

[jpearl01]

Aha. That's far more straightforward than I was expecting :-)

Looking forward to the paper!

Thanks for the clarification,

~josh