Lopper (Match Phylogenetic Datasets)
Lopper reduces pairs of phylogenetic data sets to the common set of taxa.
Quick Start
- To use Lopper, upload your data in newick or nexus (tree), comma separated vales with or without header (traits) or plain text (taxa list) format.
- Resources: documentation
Test Data
Input File(s)
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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> lopper. |
- Use lobelioids-traits.csv (trait), lobelioids-tree.txt (tree) lobelioids-list.txt (list) or lobelioids-list_mm.txt (list with mismatches) from the directory listed above as test input files. You can select any combination of these files for analysis.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
If using lobeliods-traits.csv, select file format of comma separated values with header.
If using lobelioids-tree.txt, select file format of newick
If using lobeliods-list.txt or lobelioids-list_mm.txt, select file format of list.
For the example outputs, use lobeliods-tree.txt and lobelioids-list_mm.txt. Also select to save both mismatches. Leave other parameters as default.
Output File(s)
- Expect as output (using lobelioids-tree.txt and lobelioids-list_mm.txt as input):
- matched.txt: List of matched taxa names,
- newfile.txt : Reduced phylogenetic tree,
- newfile2.txt : Reduced list of taxa names,
- lobelioids-tree_mismatches.txt: Unmatched taxa in the tree file,
- lobeliods-list_mm_mismatches.txt: Unmatched taxa in the names list.
Tool Source for App
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