View Study: loading study pg_2004...
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|Tree name (click to view)||Synthesis status||Inference method||Ingroup clade||Tree root||OTUs mapped|
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Each tab in this tool manages a different aspect of the study data. Prompts—they look like 2—identify aspects that are incomplete.
The Home tab shows metadata and lists the phylogenetic trees in the current study. Metadata is information that identifies this study and makes it easy to find, such as standard publication references, DOIs, and free-form tags. You can also add curator notes that will appear on this tab.
Trees with a synthesis status of Included or Queued have been nominated for inclusion in synthesis, generally because they best represent the conclusions of the study. Inclusion in synthesis also requires that trees be rooted correctly and have OTUs mapped.
Click on a tree name to view the tree and get more information.
You can download this study in several formats:
You can also use the Open Tree API to retrieve study data.
|File name (click to download)||Description||Size|
|Alignment data (urchins).xls Alignment data (urchins).xls||
Microsoft Excel spreadsheetSource for tree(s):
|241 KB —|
Files is a list of optional supporting files. These might include alignments, files used for inference (e.g. a BEAST XML file or MrBayes block), or lists of bootstrap trees. Tree data imported in the Home tab also appears here in its original form.
These files are not added to the study file itself; they are stored on our servers pending transfer to a permanent data repository (this feature not yet complete.)
|Original name||Mapped to taxon|
|...mapping now... Failed mapping MAPPED LABEL|
This is a list of all leaf labels, representing OTUs (operational taxonomic units), in trees in this study. For a tree to contribute to the synthetic tree, OTUs must be mapped to taxa in the OTT (Open Tree Taxonomy).
Click the magnifying-glass icon next to any OTU to see it in the context of this study's trees.
Annotations are used to store comments and validation results related to this study. They can be added by a human curator or reviewer (coming soon), or by online validators and other programs like those listed in the Tools tab.
Annotations that refer to a particular element (like a tree or OTU) will often appear in context. You can read these by clicking on a marker like 2 (coming soon), but the list below gathers all the study's annotations in a single place.
The Analysis tab reports the results of conflict analysis - how trees in this study agree / conflict with the synthetic tree or the OpenTree Taxonomy.
In the future, there will be other analyses here. Have a suggestion? Add an issue.
This tab shows the edit history for this study: each saved version of the data, who submitted the changes, and a comment added each time. The history might include edits made in other tools or by automated software. This history is possible because we keep study files under version control in a GitHub repository.