AnGST Uploader

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1. Upload Species Tree:??
Species trees should be rooted and in Newick format. Species names should not include periods or underscores. Example Species Tree
Either upload file or upload text:
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2. Is the species tree ultrametric?:??
If the branch lengths on the provided species tree represent times, AnGST can restrict the set of possible inferred gene transfers to only those between contemporaneous lineages.
3. Upload Gene Tree (bootstrap):??
Gene trees can be rooted or unrooted. Species names and gene IDs should be delimited using either a period or an underscore. If you wish to include bootstrapped gene trees, place bootstraps on separate lines. Example Gene Tree
Either upload file or upload text:
Upload File:
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OR
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4. Penalties:??
AnGST will use event penalties to find the reconciliation with the lowest overall cost. Penalties should be real and non-negative. Different event penalties will lead to different reconciliation scenarios. Choosing event penalties is not an easy problem, and you may want to try a range of penalties. We found that when looking across a broad range of gene families and eukaryotic and prokaryotic genomes, the event penalties listed above minimized the divergence in genome size among related genomes
Horizontal Gene Transfer (HGT):
Duplication (DUP):
Loss (LOS):
Speciation (SPC):
5. (Optional) Please provide an email address for updates to AnGST:

See also: Help File (pdf), Example Files (tar.gz), AnGST Source Code (Python in tar.gz)
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Web Server Code written by Albert Wang

Citation: LA David & EJ Alm. "Rapid evolutionary innovation during an Archaean Genetic Expansion." Nature, 2010. doi:10.1038/nature09649.