[Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Phylip Base.pm, 1.6, 1.7 PhylipConf.pm, 1.7, 1.8 ProtDist.pm, 1.24, 1.25

Jason Stajich jason at pub.open-bio.org
Thu Sep 29 21:09:32 EDT 2005


Update of /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/Phylip
In directory pub.open-bio.org:/tmp/cvs-serv3950/Bio/Tools/Run/Phylo/Phylip

Modified Files:
	Base.pm PhylipConf.pm ProtDist.pm 
Log Message:
protdist works for me on phylip 3.61


Index: ProtDist.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** ProtDist.pm	30 Sep 2005 00:54:14 -0000	1.24
--- ProtDist.pm	30 Sep 2005 01:09:30 -0000	1.25
***************
*** 55,60 ****
  
  This wrapper currently supports v3.5 of phylip. There is also support
! for v3.6 although this is still experimental as v3.6 is still under
! alpha release and not all functionalities maybe supported.
  
  =head1 PARAMETERS FOR PROTDIST COMPUTATION
--- 55,59 ----
  
  This wrapper currently supports v3.5 of phylip. There is also support
! for v3.6.
  
  =head1 PARAMETERS FOR PROTDIST COMPUTATION
***************
*** 79,82 ****
--- 78,85 ----
                    defaults to Equal
   		  (0.25,0.25,0.25,0.25) found in the phylip package.
+ 
+                   Additional models in PHYLIP 3.6
+                   PMB - Henikoff/Tillier PMB matrix
+ 	          JTT - Jones/Taylor/Thornton
  
  =head2 MULTIPLE

Index: PhylipConf.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** PhylipConf.pm	22 Sep 2005 19:26:44 -0000	1.7
--- PhylipConf.pm	30 Sep 2005 01:09:30 -0000	1.8
***************
*** 136,205 ****
                         },
           },
!   "3.6"=>{'PROTDIST'=>{'MODEL'  => {
!                                    'PAM'   =>"P\nY\n",
!                                    'KIMURA'=>"P\nP\nY\n",
!                                    'SIMILARITY'=>"P\nP\nP\nY\n",
!                                    'CAT'   =>"P\nP\nP\nP\n",
!                                    'JTT'   =>"Y\n"
!                                    },
!                       'GENCODE'=>  {
!                                    'ALLOWED'=>"UMVFY",
!                                    'OPTION' =>"U\n"
!                                    },
!                       'CATEGORY'=>{
!                                    'ALLOWED'=>"CHG",
!                                    'OPTION' =>"A\n"
!                                   },
!                       'PROBCHANGE'=>"E\n",
!                       'TRANS'     =>"T\n",
!                       'FREQ'      =>"F\n",
!                       'WEIGHTS'   =>"W\n",
!                       'SUBMIT'    => "Y\n",
!                       'MULTIPLE'  =>"M\nD\n",
!                      },
!           'NEIGHBOR'=>{ 'TYPE'    =>{
!                                      'UPGMA'=>"N\n",
!                                     },
!                         'OUTGROUP'=>"O\n",
!                         'LOWTRI'  =>"L\n",
!                         'UPPTRI'  =>"R\n",
!                         'SUBREP'  =>"S\n",
!                         'JUMBLE'  =>"J\n",
!                         'SUBMIT'    =>"Y\n",
!                         'MULTIPLE'  =>"M\n",
!                      },
!           'PROTPARS'=>{  'THRESHOLD'=>"T\n",
!                           'JUMBLE'   =>"J\n",
!                           'OUTGROUP' =>"O\n",
!                           'SUBMIT'   =>"Y\n",
!                        },
!           'SEQBOOT'=>{   'DATATYPE' =>{
!                                         'SEQUENCE'=>"",
!                                         'MORPH'   =>"D\n",
!                                         'REST'    =>"D\nD\n",
!                                         'GENEFREQ'=>"D\nD\nD\n",
!                                        },
!                           'ALLELES'  => "A\n",
!                           'PERMUTE'  => {
!                                         'BOOTSTRAP'=>"",
!                                         'JACKKNIFE'=>"J\n",
!                                         'PERMUTE'  =>"J\nJ\n",
!                                         },
!                           'REPLICATES'=>"R\n",
!                           'SUBMIT'   =>"Y\n",
!                        },
! 
!            'CONSENSE'=>{  'TYPE'     => {
!                                         'MRE'     =>"",
!                                         'STRICT'  =>"C\n",
!                                         'MR'      =>"C\nC\n",
!                                         'ML'      =>"C\nC\nC\n",
!                                         },
!                           'ROOTED'   => "R\n",
!                           'OUTGROUP' => "O\n",
!                           'SUBMIT'    =>"Y\n",
!                        },
!          },
! );
  
  1;
--- 136,208 ----
                         },
           },
! 	 
!   "3.6"=>{
!       'PROTDIST'=>{
! 	  'MODEL'  => {
! 	      'PMB'        =>"P\n",
! 	      'PAM'        =>"P\nP\n",
! 	      'KIMURA'     =>"P\nP\nP\n",
! 	      'CAT'        =>"P\nP\nP\nP\n",
! 	      'JTT'        =>"Y\n",
! 	  },
! 	  'GENCODE'=>  {
! 	      'ALLOWED'=>"UMVFY",
! 	      'OPTION' =>"U\n",
! 	  },
! 	  'CATEGORY'=> {
! 	      'ALLOWED'=>"CHG",
! 	      'OPTION' =>"A\n",
! 	  },
! 	  'PROBCHANGE'=>"E\n",
! 	  'TRANS'     =>"T\n",
! 	  'FREQ'      =>"F\n",
! 	  'WEIGHTS'   =>"W\n",
! 	  'SUBMIT'    => "Y\n",
! 	  'MULTIPLE'  =>"M\nD\n",
!       },
!       'NEIGHBOR'=>{ 'TYPE'    =>{
! 	  'UPGMA'=>"N\n",
!       },
! 		    'OUTGROUP'=>"O\n",
! 		    'LOWTRI'  =>"L\n",
! 		    'UPPTRI'  =>"R\n",
! 		    'SUBREP'  =>"S\n",
! 		    'JUMBLE'  =>"J\n",
! 		    'SUBMIT'    =>"Y\n",
! 		    'MULTIPLE'  =>"M\n",
! 		},
!       'PROTPARS'=>{  'THRESHOLD'=>"T\n",
! 		     'JUMBLE'   =>"J\n",
! 		     'OUTGROUP' =>"O\n",
! 		     'SUBMIT'   =>"Y\n",
! 		 },
!       'SEQBOOT'=>{   'DATATYPE' =>{
! 	  'SEQUENCE'=>"",
! 	  'MORPH'   =>"D\n",
! 	  'REST'    =>"D\nD\n",
! 	  'GENEFREQ'=>"D\nD\nD\n",
!       },
! 		     'ALLELES'  => "A\n",
! 		     'PERMUTE'  => {
! 			 'BOOTSTRAP'=>"",
! 			 'JACKKNIFE'=>"J\n",
! 			 'PERMUTE'  =>"J\nJ\n",
! 		     },
! 		     'REPLICATES'=>"R\n",
! 		     'SUBMIT'   =>"Y\n",
! 		 },
!       
!       'CONSENSE'=>{  'TYPE'     => {
! 	  'MRE'     =>"",
! 	  'STRICT'  =>"C\n",
! 	  'MR'      =>"C\nC\n",
! 	  'ML'      =>"C\nC\nC\n",
!       },
! 		     'ROOTED'   => "R\n",
! 		     'OUTGROUP' => "O\n",
! 		     'SUBMIT'    =>"Y\n",
! 		 },
!   },
! 	 );
  
  1;

Index: Base.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/Phylip/Base.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** Base.pm	28 Mar 2003 22:42:08 -0000	1.6
--- Base.pm	30 Sep 2005 01:09:30 -0000	1.7
***************
*** 90,94 ****
  BEGIN {
      %DEFAULT = ( 
!      'VERSION'   => $ENV{'PHYLIPVERSION'} || '3.5',
  		 );
      %FILENAME = %Bio::Tools::Run::Phylo::Phylip::PhylipConf::FileName;
--- 90,94 ----
  BEGIN {
      %DEFAULT = ( 
!      'VERSION'   => $ENV{'PHYLIPVERSION'} || '3.6',
  		 );
      %FILENAME = %Bio::Tools::Run::Phylo::Phylip::PhylipConf::FileName;



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