TreeDist
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ms609
Calculate distances between phylogenetic trees in R
HI there, I have been comparing some subsampled simulations I have to their true tree. I want to use the CID and MSID tree distance metrics as suggested in Smith...
Branch: max-inf-cons-tree Reading: https://www.biorxiv.org/content/10.1101/2024.02.20.581316v1
Linked branch: spr-dist Reading list: - [ ] https://journals.sagepub.com/doi/pdf/10.4137/EBO.S9657 - [ ] https://www.computer.org/csdl/journal/tb/2019/03/08291143/13rRUwInv33 [10.1109/TCBB.2018.2802911](https://doi.ieeecomputersociety.org/10.1109/TCBB.2018.2802911) = https://ieeexplore.ieee.org/abstract/document/8291143 = [10.1109/TCBB.2018.2802911](https://doi.org/10.1109/TCBB.2018.2802911) - [ ] https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=8291143 - [ ] [A Cluster Reduction for Computing...
[On Defining and Finding Islands of Trees and Mitigating Large Island Bias ](https://doi.org/10.1093/sysbio/syab015)
# Important: **DO NOT PULL** Created PR to check GHA for memory leaks. Not intended for production.
It's potentially confusing when distances of zero are computed with no message, e.g. where tree 1 contains underscores and tree 2 spaces. Perhaps throw warning when comparing trees with different...
in `app.R`, `thinnedTrees()` is naively defined as `as.integer(seq(keptRange()[1], keptRange()[2], by = 2 ^ input$thinTrees))` This assumes that trees have been loaded from a single file. Otherwise the numbers are garbage....