Can autolin be used in non-parsimony trees?

jmcbroome / autolin

Repository containing a method for automatically identifying pathogen lineages from a phylogeny.

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Can autolin be used in non-parsimony trees? #7

Closed santanaw closed 2 months ago

santanaw commented 4 months ago

Hi @jmcbroome,

Many thanks for developing autolin! I did noticed that autolin can be used with parsimony phylogenies, but I wonder if it can be used on approximately-maximum-likelihood phylogenetic trees?

Many thanks for any information.

jmcbroome commented 2 months ago

Sorry for the slow response. Yes, the method can apply to any numerical branch length; however, the idea of representing clusters with distinct shared genetic sequences doesn't quite apply in the same way. The code should just work out of the box on it.