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Correct params and switches

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1 parent d8572b5 commit 6e9d92864b5acb54ff8d301ac349fb5e1f54d12c @bosborne bosborne committed Feb 8, 2012
Showing with 7 additions and 2 deletions.
  1. +7 −2 lib/Bio/Tools/Run/Alignment/
@@ -116,9 +116,14 @@ use base qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
our %DEFAULTS = ( 'AFORMAT' => 'fasta' );
our @MUSCLE_PARAMS = qw(in out tree1 log loga scorefile gapopen seqtype
- maxmb maxhours maxiters kband in1 in2 usetree usetree_nowarn);
+ maxmb maxhours maxiters kband in1 in2 usetree usetree_nowarn
+ weight1 weight2 smoothwindow SUEFF smoothscoreceil root1 root2
+ refinewindow physout phyiout objscore minsmoothscore minbestcolscore
+ hydrofactor hydro anchorspacing center cluster1 cluster2 clwout diagbreak
+ diaglength diagmargin distance1 distance2);
our @MUSCLE_SWITCHES = qw(quiet verbose diags refine stable group
- clw clwstrict msf);
+ clw clwstrict msf brenner cluster dimer fasta html le anchors noanchors
+ phyi phys profile refinew sp spscore spn sv);
our $PROGRAM_NAME = 'muscle';
our $PROGRAM_DIR = Bio::Root::IO->catfile($ENV{MUSCLEDIR}) if $ENV{MUSCLEDIR};

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