FastTree2 (USER MANUAL UNDER DEVELOPMENT)

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FastTree Dispatcher 2

Quick Start

• To use AppName, upload  upload your data in ___ format.Resources: <link to source documentation>fasta alignment format, e.g. from ClustalW2.
• Resources: http://rpackages.ianhowson.com/rforge/rPlant/man/Fasttree.html

Test Data

Input File(s)

Use TerriblyIncomprehensible.txt from http://mirrors.iplantcollaborative.org/example_data/proper_location_here/filename.extension
and HorriblyWritten.txt from http://mirrors.iplantcollaborative.org/example_data/proper_location_here/filename.extension as test data. Import from URL to get the data into your Discovery Environment account.

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.

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Use fasta.aln which is found in the example data section of the Data Store: Community Data > iplantcollaborative > example_data > fasttree2 > input

Parameters Used in App

• Default parameters only, no further configuration needed.

OR

• Use these parameters within the DE app interface:
• parameter name - value/setting
• parameter name - value/setting

Output File(s)

Expect a txt  a .nwk file as output.Name any sample  

The output file (s) and provide the link to their location, as you did with the input file(s). These will be used to confirm the app works. Without these files, no confirmation will be possible.

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from the test data is found here: Community Data > iplantcollaborative > example_data > fasttree2 > output > fasttree.nwk.

Tool Source for App

• http://replacefinzi.psych.with.URL_for_tool.orgupenn.edu/library/rPlant/html/Fasttree.html