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Muscle Named Outputs

Muscle Named Outputs is an integration of Muscle that includes named outputs.  Named outputs are required for the construction of simple automated workflows.  Output formats

Include Page
phylip interleaved, phylip sequential, fasta, and clustalw

Quick Start

  • To use: select a fasta file as an input
  • Run!

Test Data

Info

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> muscle_named_outputs.

Input File(s)

Use jasmonin_homologs_proteins.faa from the directory above as test input.

Parameters Used in App

The only parameter you may wish to set is the sequence type (protein, dna, rna) of the data in the input fasta file.  By default, the "auto" option is used which will try to auto detect the sequence type.

Output File(s)

  • phylip_interleaved.aln : alignment in phylip interleaved format
  • phylip_sequential.aln : alignment in phylip sequential format
  • fasta.aln : alignment in fasta format
  • clustalw.aln : alignment in clustalw format

Tool Source for App

http://www.drive5.com/muscle/muscle_userguide3.8.html

docs:_DE_archived_apps_blurb
docs:_DE_archived_apps_blurb