Generalized quartet distance

[kalvinchang]

Hi. My research lab is currently looking for implementations of generalized quartet distance and was wondering where you obtained your implementation of GQD.

In gqd.py, I see that you call "/home/tarakark/tools/qdist/qdist," so I was wondering if you could point us to where you got qdist from.

Thanks!!

[PhyloStar]

Hi. Here is the link: https://birc.au.dk/software/qdist

[kalvinchang]

Thank you!

[kalvinchang]

Our group had a question about GQD.

In Rama et al (2018), you define the GQD as the number of butterflies that differ between the gold and hypothesis tree divided by the number of butterflies in the gold tree.

When calculating the number of butterflies that differ between the gold and hypothesis tree, do we only include the butterflies in the GOLD tree that do not match the hypothesis?

i.e. Can we calculate the numerator of GQD as # gold butterflies - # butterflies that agree between gold and hypothesis

OR

Should we be calculating different butterflies as # butterflies in gold + # butterflies in hyp - 2 * # agreeing butterflies

(Im leaning towards the first option)

(Unfortunately, the newer version of qDist tqDist does not return the different butterflies between the two)