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justsz / Mastodon

a Java tool for the summary and visualization of large sets of phylogenetic trees

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Add burn-in and sampling option

justsz opened this issue · comments

commented

Burn-in : discard first n trees generated by MCMC
Sampling : take every n-th tree from the set

commented

Added Burn-in option. It is the more useful one in our case I think, because having many trees isn't thaaat much of an issue with speed.
The burn-in procedure is a bit wasteful though, as the trees are indeed being read, just not converted to to BitTrees in the BitTreeSystem. There's probably an easy way to detect a tree in a text file, then skip over it.