The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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ProgressiveMauve

ProgressiveMauve is a multiple whole genome alignment.

progressiveMauve chloroplast_Aethionema_cordifolium.faa chloroplast_Aethionema_grandiflorum.faa chloroplast_Arabidopsis_thaliana.faa > mauve.alignment

Quick Start

  • To use ProgressiveMauve, upload your data in fasta format.
  • Resources: documentation

Test Data

All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > progressivemauve

Input File(s)

Parameters Used in App

  • This app has no additional options.  The default progressiveMauve options are used.

Output File(s)

  • Alignment file will be named mauve.alignment. Additional outputs generated are
  • Example alignment file generated use the above example input files: mauve.alignment 
    • The command-line for generating the output file from the input files is
    • Additional outputs include a .sslist file for all fasta files used in alignment, the alignment backbone and a .bbcols file.

Tool Source for App

Name: Mauve
Description: Multiple Genome Sequence Alignment
Version: 2.3.1
User Guide: http://asap.ahabs.wisc.edu/mauve/
Source-code downloaded from: http://asap.ahabs.wisc.edu/mauve/