Synthesis release

   

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Release notes

A fuller release history (including early draft versions) is available in the germinator documentation:

Open Tree of Life version 12.3

Version 12.3 of the synthetic tree was generated on 23 December 2019 using the propinquity pipeline.

Downloads

There are two downloads. The first (smaller download) contain only tree and annotations files. The second (larger download) is the full output from the synthesis procedure, including documentation. You can also browse the full output.

  • Tree and annotations : Several versions of the synthetic tree, along with the annotations file. See the enclosed README for details. (compressed tar archive; 40 Mbytes)
  • All pipeline outputs : Outputs and documentation from all stages of the synthesis pipeline. Or, you can browse the output rather than downloading. (compressed tar archive; 301 Mbytes)

Release notes

Changes in inputs

  • based on OTT 3.2 instead of OTT 3.1
  • 6 new input trees.

Changes in output

  version11.4 version12.3 change
total tips 2852504 2391916 -460588
tips from phylogeny 87682 87740 58
internal nodes in taxonomy 218186 224063 5877
internal nodes from phylogeny 79982 80048 66
broken taxa 5635 5665 30
subproblems 9860 9889 29

Comments

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  • So how does one download it and view it?on GitHub

    I have downloaded the files (?) but I don't know what program it needs to view it

    Patricia - 3 years agoHide comments

    • Hi Patricia - there aren't any off-the-shelf programs that will be able to visualise a phylogenetic tree of this size. As far as I know, the only programs that have attempted this are https://lifemap-ncbi.univ-lyon1.fr">LifeMap and https://github.com/OneZoom/OZtree">OneZoom (disclaimer - I'm involved in OneZoom). Otherwise you might want to trim the tree down to a manageable size somehow. Even reading it in to a phylogenetic library such as Dendropy is likely to bung up your computer for many minutes or (possibly) hours, and take up quite a lot of RAM.

      What are you trying to do with the files?

      Yan Wong - 2 years ago

    • Archaeopteryx tree viewer can manage to display these files, though slow on the full synthesis

      Douglas Chesters - 1 year ago