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rbouckaert / DensiTree

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tip numbers #9

Open xiaoyezao opened 3 years ago

xiaoyezao commented 3 years ago

Can DensiTree deal with tree sets that have different numbers of tips in individual trees?

rbouckaert commented 3 years ago

Yes, DensiTree can deal with sets with different numbers of tips, provided the first tree contains all tips.

RhettRautsaw commented 2 years ago

Does this mean that if I load in a species tree and then a few thousand gene trees each with missing tips/taxa, that DensiTree should be able to handle that? I'm trying to do this, but it doesn't seem to work so I feel like I'm misunderstanding what this issue meant.

rbouckaert commented 2 years ago

Maybe you need to set burn-in to zero in order to pick up the first tree in the set? For newick tree files, the first tree after burn-in in the set must contain all tip names of the set of all the gene tree tips. Hope this makes sense.

AlesBucek commented 1 year ago

Yes, DensiTree can deal with sets with different numbers of tips, provided the first tree contains all tips.

Hi! This seems to be in conflict with the issue "Loading file with missing taxa needs improvement" where you described that loading trees which are missing some tips results in error: "When loading a set of trees where not all taxa are present in all trees, DensiTree cannot handle the data".