Usecase: GreenPhylDB and tree pattern matching
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First of all, go to the GreenPhylDB tree pattern matching page: https://www.greenphyl.org/cgi-bin/treepattern.cgi . Then, then build the pattern on the top figure, using « duplication », « speciation » and « taxa/cardinality » tools. Or just copy past and load, in the file menu, the following textual pattern:
((HORVU:-1[<R>HORVU</R><S>1</S>],HORVU:-1[<R>HORVU</R><S>2</S>])D:-1[<R>HORVU</R><IR>3</IR>],ORYSA:-1[<R>ORYSA</R><S>3</S>])S:-1;. The pattern should be identical to the pattern displayed on the top figure. -
Then click on « search pattern ». In the result list, click on the « GP000072 » family (the third in the list).
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Scroll down in the tree in order to retrieve the sequences displayed in the figure (or search on of them, i.e HORVU5Hr1G004510.1, using the functionality of your web browser).
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Then you can click on either of the three sequences, to be redirected on the corresponding GreenPhylDB webpage.
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On the GreenPhylDB page, you can display the proteic domains, and observe the same diversity that is displayed on the figure, clicking on the domain pattern tab.
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Finally, going back to the result list, you can click on the « full results » link, download the CSV, and display it on any spreadsheet program.