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)

• Select two or more fasta files for alignment.  Must be DNA sequence.
  • To generate the example outputs provided, use all 3 files.
• Test files:
  • Use chloroplast_Aethionema_cordifolium.faa
  • Use chloroplast_Aethionema_grandiflorum.faa
  • Use chloroplast_Arabidopsis_thaliana.faa

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

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

  • 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/