<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<presets>\r
- <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>\r
- <preset>\r
- <name>Protein alignment(Fastest speed)</name>\r
- <description>Fastest possible speed for protein sequences. Gives acceptable quality alignments for closely related sequences</description>\r
- <optlist>\r
- <option>-maxiters 1</option>\r
- <option>-diags</option>\r
- <option>-sv</option>\r
- <option>-distance1 kbit20_3</option>\r
- </optlist>\r
- </preset>\r
- <preset>\r
- <name>Nucleotide alignment(Fastest speed)</name>\r
- <description>Fastest possible speed for nucleotide sequences. Gives acceptable quality alignments for closely related sequences</description>\r
- <optlist>\r
- <option>-maxiters 1</option>\r
- <option>-diags</option>\r
- </optlist>\r
- </preset>\r
- <preset>\r
- <name>Large alignments (balanced)</name>\r
- <description>A large number of sequences (a few thousand), or very long sequences, \r
- then the default settings of may be too slow for practical use. \r
- A good compromise between speed and accuracy is to run just the first two iterations of \r
- the algorithm</description>\r
- <optlist>\r
- <option>-maxiters 2</option>\r
- </optlist>\r
- </preset>\r
+ <runnerClassName>compbio.runner.msa.Muscle</runnerClassName>\r
+\r
+ <preset>\r
+ <name>Protein alignment(Fastest speed)</name>\r
+ <description>\r
+ Fastest possible speed for protein sequences. Gives acceptable quality \r
+ alignments for closely related sequences\r
+ </description>\r
+ <optlist>\r
+ <option>-maxiters 1</option>\r
+ <option>-diags</option>\r
+ <option>-sv</option>\r
+ <option>-distance1 kbit20_3</option>\r
+ </optlist>\r
+ </preset>\r
+\r
+ <preset>\r
+ <name>Nucleotide alignment(Fastest speed)</name>\r
+ <description>\r
+ Fastest possible speed for nucleotide sequences. Gives acceptable quality \r
+ alignments for closely related sequences\r
+ </description>\r
+ <optlist>\r
+ <option>-maxiters 1</option>\r
+ <option>-diags</option>\r
+ </optlist>\r
+ </preset>\r
+\r
+ <preset>\r
+ <name>Large alignments (balanced)</name>\r
+ <description>\r
+ A large number of sequences (a few thousand), or very long sequences, then the default \r
+ settings of may be too slow for practical use. A good compromise between speed and \r
+ accuracy is to run just the first two iterations of the algorithm.\r
+ </description>\r
+ <optlist>\r
+ <option>-maxiters 2</option>\r
+ </optlist>\r
+ </preset>\r
</presets>\r