Skip to content
This repository
Browse code

sync with trunk

svn path=/bioperl-run/branches/branch-1-6/; revision=16221
  • Loading branch information...
commit 4133c9a12e608102ec20537519934c531fe9c077 1 parent 3250289
authored September 30, 2009

Showing 98 changed files with 419 additions and 393 deletions. Show diff stats Hide diff stats

  1. 19  Changes
  2. 8  lib/Bio/Factory/EMBOSS.pm
  3. 8  lib/Bio/Installer/Clustalw.pm
  4. 8  lib/Bio/Installer/EMBOSS.pm
  5. 8  lib/Bio/Installer/Generic.pm
  6. 8  lib/Bio/Installer/Hyphy.pm
  7. 8  lib/Bio/Installer/Muscle.pm
  8. 8  lib/Bio/Installer/PAML.pm
  9. 8  lib/Bio/Installer/Probcons.pm
  10. 8  lib/Bio/Installer/SLR.pm
  11. 8  lib/Bio/Installer/TCoffee.pm
  12. 8  lib/Bio/Tools/Run/Alignment/Amap.pm
  13. 8  lib/Bio/Tools/Run/Alignment/Blat.pm
  14. 8  lib/Bio/Tools/Run/Alignment/Clustalw.pm
  15. 8  lib/Bio/Tools/Run/Alignment/DBA.pm
  16. 2  lib/Bio/Tools/Run/Alignment/Exonerate.pm
  17. 8  lib/Bio/Tools/Run/Alignment/Kalign.pm
  18. 8  lib/Bio/Tools/Run/Alignment/Lagan.pm
  19. 8  lib/Bio/Tools/Run/Alignment/MAFFT.pm
  20. 8  lib/Bio/Tools/Run/Alignment/Muscle.pm
  21. 8  lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
  22. 8  lib/Bio/Tools/Run/Alignment/Probalign.pm
  23. 8  lib/Bio/Tools/Run/Alignment/Probcons.pm
  24. 8  lib/Bio/Tools/Run/Alignment/Proda.pm
  25. 8  lib/Bio/Tools/Run/Alignment/Sim4.pm
  26. 8  lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
  27. 10  lib/Bio/Tools/Run/Alignment/TCoffee.pm
  28. 8  lib/Bio/Tools/Run/Analysis.pm
  29. 8  lib/Bio/Tools/Run/Analysis/soap.pm
  30. 8  lib/Bio/Tools/Run/AnalysisFactory.pm
  31. 8  lib/Bio/Tools/Run/AnalysisFactory/soap.pm
  32. 8  lib/Bio/Tools/Run/Cap3.pm
  33. 8  lib/Bio/Tools/Run/Coil.pm
  34. 8  lib/Bio/Tools/Run/EMBOSSApplication.pm
  35. 8  lib/Bio/Tools/Run/EMBOSSacd.pm
  36. 8  lib/Bio/Tools/Run/ERPIN.pm
  37. 8  lib/Bio/Tools/Run/Ensembl.pm
  38. 8  lib/Bio/Tools/Run/Eponine.pm
  39. 8  lib/Bio/Tools/Run/FootPrinter.pm
  40. 8  lib/Bio/Tools/Run/Genemark.pm
  41. 8  lib/Bio/Tools/Run/Genewise.pm
  42. 8  lib/Bio/Tools/Run/Genscan.pm
  43. 8  lib/Bio/Tools/Run/Glimmer.pm
  44. 8  lib/Bio/Tools/Run/Hmmer.pm
  45. 13  lib/Bio/Tools/Run/Infernal.pm
  46. 8  lib/Bio/Tools/Run/MCS.pm
  47. 8  lib/Bio/Tools/Run/Match.pm
  48. 8  lib/Bio/Tools/Run/Mdust.pm
  49. 8  lib/Bio/Tools/Run/Meme.pm
  50. 8  lib/Bio/Tools/Run/Phrap.pm
  51. 8  lib/Bio/Tools/Run/Phylo/Gerp.pm
  52. 8  lib/Bio/Tools/Run/Phylo/Gumby.pm
  53. 8  lib/Bio/Tools/Run/Phylo/Hyphy/Base.pm
  54. 8  lib/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
  55. 8  lib/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
  56. 8  lib/Bio/Tools/Run/Phylo/Hyphy/REL.pm
  57. 8  lib/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
  58. 8  lib/Bio/Tools/Run/Phylo/LVB.pm
  59. 8  lib/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
  60. 8  lib/Bio/Tools/Run/Phylo/Njtree/Best.pm
  61. 8  lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm
  62. 8  lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm
  63. 8  lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm
  64. 8  lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm
  65. 8  lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
  66. 8  lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
  67. 8  lib/Bio/Tools/Run/Phylo/Phylip/Base.pm
  68. 8  lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm
  69. 8  lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
  70. 8  lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
  71. 8  lib/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
  72. 8  lib/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
  73. 8  lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
  74. 8  lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
  75. 8  lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
  76. 8  lib/Bio/Tools/Run/Phylo/PhyloBase.pm
  77. 8  lib/Bio/Tools/Run/Phylo/Phyml.pm
  78. 8  lib/Bio/Tools/Run/Phylo/QuickTree.pm
  79. 8  lib/Bio/Tools/Run/Phylo/SLR.pm
  80. 8  lib/Bio/Tools/Run/Phylo/Semphy.pm
  81. 8  lib/Bio/Tools/Run/Primate.pm
  82. 8  lib/Bio/Tools/Run/Primer3.pm
  83. 8  lib/Bio/Tools/Run/Prints.pm
  84. 8  lib/Bio/Tools/Run/Profile.pm
  85. 8  lib/Bio/Tools/Run/Promoterwise.pm
  86. 8  lib/Bio/Tools/Run/Pseudowise.pm
  87. 8  lib/Bio/Tools/Run/RNAMotif.pm
  88. 8  lib/Bio/Tools/Run/RepeatMasker.pm
  89. 8  lib/Bio/Tools/Run/Seg.pm
  90. 8  lib/Bio/Tools/Run/Signalp.pm
  91. 8  lib/Bio/Tools/Run/Simprot.pm
  92. 8  lib/Bio/Tools/Run/TigrAssembler.pm
  93. 8  lib/Bio/Tools/Run/TribeMCL.pm
  94. 8  lib/Bio/Tools/Run/Vista.pm
  95. 8  lib/Bio/Tools/Run/tRNAscanSE.pm
  96. 20  t/Infernal.t
  97. 8  t/data/purine.added.fa
  98. 12  t/gmap-run.t
19  Changes
@@ -4,17 +4,24 @@ Revision history for bioperl-run modules
4 4
 Full details of changes between all versions are available online at:
5 5
 http://www.bioperl.org/wiki/Change_log
6 6
 
  7
+1.6.2 Release
  8
+
  9
+* [bug 2713] - Bio::Tools::Run::Infernal now works with Infernal 1.0 (older
  10
+  versions deprecated) [cjfields]
  11
+* Bio::Tools::Run::Alignment::Gmap added [hartzell]
  12
+* [bug 2798] - patch to fix clustalw premature file unlinking error [Wei Zhou]
  13
+
7 14
 1.6.0 Release
8 15
    
9  
-   o All Pise and Pise-related modules and scripts have been moved to the
10  
-     new bioperl-pise repository. The Pise service is no longer available and
11  
-     has been replaced by Mobyle.  They have been retained as one can still
12  
-     install a Pise server, and as these modules can possibly be used to create
13  
-     a new BioPerl API for Mobyle.
  16
+* All Pise and Pise-related modules and scripts have been moved to the new
  17
+  bioperl-pise repository. The Pise service is no longer available and has been
  18
+  replaced by Mobyle. They have been retained as one can still install a Pise
  19
+  server, and as these modules can possibly be used to create a new BioPerl API
  20
+  for Mobyle.
14 21
 
15 22
 1.5.2 Release in sync with bioperl core
16 23
 
17  
-   o Several wrappers updated for newer versions of the programs.
  24
+* Several wrappers updated for newer versions of the programs.
18 25
    
19 26
 1.5.1 Release in sync with bioperl core
20 27
 
8  lib/Bio/Factory/EMBOSS.pm
@@ -70,11 +70,11 @@ Bioperl mailing lists  Your participation is much appreciated.
70 70
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
71 71
 
72 72
 =head2 Support 
73  
- 
  73
+
74 74
 Please direct usage questions or support issues to the mailing list:
75  
-  
76  
-L<bioperl-l@bioperl.org>
77  
-  
  75
+
  76
+I<bioperl-l@bioperl.org>
  77
+
78 78
 rather than to the module maintainer directly. Many experienced and 
79 79
 reponsive experts will be able look at the problem and quickly 
80 80
 address it. Please include a thorough description of the problem 
8  lib/Bio/Installer/Clustalw.pm
@@ -35,11 +35,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
35 35
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
36 36
 
37 37
 =head2 Support 
38  
- 
  38
+
39 39
 Please direct usage questions or support issues to the mailing list:
40  
-  
41  
-L<bioperl-l@bioperl.org>
42  
-  
  40
+
  41
+I<bioperl-l@bioperl.org>
  42
+
43 43
 rather than to the module maintainer directly. Many experienced and 
44 44
 reponsive experts will be able look at the problem and quickly 
45 45
 address it. Please include a thorough description of the problem 
8  lib/Bio/Installer/EMBOSS.pm
@@ -35,11 +35,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
35 35
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
36 36
 
37 37
 =head2 Support 
38  
- 
  38
+
39 39
 Please direct usage questions or support issues to the mailing list:
40  
-  
41  
-L<bioperl-l@bioperl.org>
42  
-  
  40
+
  41
+I<bioperl-l@bioperl.org>
  42
+
43 43
 rather than to the module maintainer directly. Many experienced and 
44 44
 reponsive experts will be able look at the problem and quickly 
45 45
 address it. Please include a thorough description of the problem 
8  lib/Bio/Installer/Generic.pm
@@ -34,11 +34,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
34 34
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
35 35
 
36 36
 =head2 Support 
37  
- 
  37
+
38 38
 Please direct usage questions or support issues to the mailing list:
39  
-  
40  
-L<bioperl-l@bioperl.org>
41  
-  
  39
+
  40
+I<bioperl-l@bioperl.org>
  41
+
42 42
 rather than to the module maintainer directly. Many experienced and 
43 43
 reponsive experts will be able look at the problem and quickly 
44 44
 address it. Please include a thorough description of the problem 
8  lib/Bio/Installer/Hyphy.pm
@@ -35,11 +35,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
35 35
   http://bioperl.org/MailList.shtml  - About the mailing lists
36 36
 
37 37
 =head2 Support 
38  
- 
  38
+
39 39
 Please direct usage questions or support issues to the mailing list:
40  
-  
41  
-L<bioperl-l@bioperl.org>
42  
-  
  40
+
  41
+I<bioperl-l@bioperl.org>
  42
+
43 43
 rather than to the module maintainer directly. Many experienced and 
44 44
 reponsive experts will be able look at the problem and quickly 
45 45
 address it. Please include a thorough description of the problem 
8  lib/Bio/Installer/Muscle.pm
@@ -35,11 +35,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
35 35
   http://bioperl.org/MailList.shtml  - About the mailing lists
36 36
 
37 37
 =head2 Support 
38  
- 
  38
+
39 39
 Please direct usage questions or support issues to the mailing list:
40  
-  
41  
-L<bioperl-l@bioperl.org>
42  
-  
  40
+
  41
+I<bioperl-l@bioperl.org>
  42
+
43 43
 rather than to the module maintainer directly. Many experienced and 
44 44
 reponsive experts will be able look at the problem and quickly 
45 45
 address it. Please include a thorough description of the problem 
8  lib/Bio/Installer/PAML.pm
@@ -34,11 +34,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
34 34
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
35 35
 
36 36
 =head2 Support 
37  
- 
  37
+
38 38
 Please direct usage questions or support issues to the mailing list:
39  
-  
40  
-L<bioperl-l@bioperl.org>
41  
-  
  39
+
  40
+I<bioperl-l@bioperl.org>
  41
+
42 42
 rather than to the module maintainer directly. Many experienced and 
43 43
 reponsive experts will be able look at the problem and quickly 
44 44
 address it. Please include a thorough description of the problem 
8  lib/Bio/Installer/Probcons.pm
@@ -35,11 +35,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
35 35
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
36 36
 
37 37
 =head2 Support 
38  
- 
  38
+
39 39
 Please direct usage questions or support issues to the mailing list:
40  
-  
41  
-L<bioperl-l@bioperl.org>
42  
-  
  40
+
  41
+I<bioperl-l@bioperl.org>
  42
+
43 43
 rather than to the module maintainer directly. Many experienced and 
44 44
 reponsive experts will be able look at the problem and quickly 
45 45
 address it. Please include a thorough description of the problem 
8  lib/Bio/Installer/SLR.pm
@@ -35,11 +35,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
35 35
   http://bioperl.org/MailList.shtml  - About the mailing lists
36 36
 
37 37
 =head2 Support 
38  
- 
  38
+
39 39
 Please direct usage questions or support issues to the mailing list:
40  
-  
41  
-L<bioperl-l@bioperl.org>
42  
-  
  40
+
  41
+I<bioperl-l@bioperl.org>
  42
+
43 43
 rather than to the module maintainer directly. Many experienced and 
44 44
 reponsive experts will be able look at the problem and quickly 
45 45
 address it. Please include a thorough description of the problem 
8  lib/Bio/Installer/TCoffee.pm
@@ -35,11 +35,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
35 35
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
36 36
 
37 37
 =head2 Support 
38  
- 
  38
+
39 39
 Please direct usage questions or support issues to the mailing list:
40  
-  
41  
-L<bioperl-l@bioperl.org>
42  
-  
  40
+
  41
+I<bioperl-l@bioperl.org>
  42
+
43 43
 rather than to the module maintainer directly. Many experienced and 
44 44
 reponsive experts will be able look at the problem and quickly 
45 45
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Alignment/Amap.pm
@@ -110,11 +110,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
110 110
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
111 111
 
112 112
 =head2 Support 
113  
- 
  113
+
114 114
 Please direct usage questions or support issues to the mailing list:
115  
-  
116  
-L<bioperl-l@bioperl.org>
117  
-  
  115
+
  116
+I<bioperl-l@bioperl.org>
  117
+
118 118
 rather than to the module maintainer directly. Many experienced and 
119 119
 reponsive experts will be able look at the problem and quickly 
120 120
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Alignment/Blat.pm
@@ -37,11 +37,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
37 37
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
38 38
 
39 39
 =head2 Support 
40  
- 
  40
+
41 41
 Please direct usage questions or support issues to the mailing list:
42  
-  
43  
-L<bioperl-l@bioperl.org>
44  
-  
  42
+
  43
+I<bioperl-l@bioperl.org>
  44
+
45 45
 rather than to the module maintainer directly. Many experienced and 
46 46
 reponsive experts will be able look at the problem and quickly 
47 47
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Alignment/Clustalw.pm
@@ -321,11 +321,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
321 321
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
322 322
 
323 323
 =head2 Support 
324  
- 
  324
+
325 325
 Please direct usage questions or support issues to the mailing list:
326  
-  
327  
-L<bioperl-l@bioperl.org>
328  
-  
  326
+
  327
+I<bioperl-l@bioperl.org>
  328
+
329 329
 rather than to the module maintainer directly. Many experienced and 
330 330
 reponsive experts will be able look at the problem and quickly 
331 331
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Alignment/DBA.pm
@@ -67,11 +67,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
67 67
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
68 68
 
69 69
 =head2 Support 
70  
- 
  70
+
71 71
 Please direct usage questions or support issues to the mailing list:
72  
-  
73  
-L<bioperl-l@bioperl.org>
74  
-  
  72
+
  73
+I<bioperl-l@bioperl.org>
  74
+
75 75
 rather than to the module maintainer directly. Many experienced and 
76 76
 reponsive experts will be able look at the problem and quickly 
77 77
 address it. Please include a thorough description of the problem 
2  lib/Bio/Tools/Run/Alignment/Exonerate.pm
@@ -66,7 +66,7 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
66 66
 
67 67
 Please direct usage questions or support issues to the mailing list:
68 68
 
69  
-L<bioperl-l@bioperl.org>
  69
+I<bioperl-l@bioperl.org>
70 70
 
71 71
 rather than to the module maintainer directly. Many experienced and
72 72
 reponsive experts will be able look at the problem and quickly
8  lib/Bio/Tools/Run/Alignment/Kalign.pm
@@ -80,11 +80,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
80 80
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
81 81
 
82 82
 =head2 Support 
83  
- 
  83
+
84 84
 Please direct usage questions or support issues to the mailing list:
85  
-  
86  
-L<bioperl-l@bioperl.org>
87  
-  
  85
+
  86
+I<bioperl-l@bioperl.org>
  87
+
88 88
 rather than to the module maintainer directly. Many experienced and 
89 89
 reponsive experts will be able look at the problem and quickly 
90 90
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Alignment/Lagan.pm
@@ -97,11 +97,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
97 97
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
98 98
 
99 99
 =head2 Support 
100  
- 
  100
+
101 101
 Please direct usage questions or support issues to the mailing list:
102  
-  
103  
-L<bioperl-l@bioperl.org>
104  
-  
  102
+
  103
+I<bioperl-l@bioperl.org>
  104
+
105 105
 rather than to the module maintainer directly. Many experienced and 
106 106
 reponsive experts will be able look at the problem and quickly 
107 107
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Alignment/MAFFT.pm
@@ -38,11 +38,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
38 38
   http://bioperl.org/MailList.html - About the mailing lists
39 39
 
40 40
 =head2 Support 
41  
- 
  41
+
42 42
 Please direct usage questions or support issues to the mailing list:
43  
-  
44  
-L<bioperl-l@bioperl.org>
45  
-  
  43
+
  44
+I<bioperl-l@bioperl.org>
  45
+
46 46
 rather than to the module maintainer directly. Many experienced and 
47 47
 reponsive experts will be able look at the problem and quickly 
48 48
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Alignment/Muscle.pm
@@ -78,11 +78,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
78 78
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
79 79
 
80 80
 =head2 Support 
81  
- 
  81
+
82 82
 Please direct usage questions or support issues to the mailing list:
83  
-  
84  
-L<bioperl-l@bioperl.org>
85  
-  
  83
+
  84
+I<bioperl-l@bioperl.org>
  85
+
86 86
 rather than to the module maintainer directly. Many experienced and 
87 87
 reponsive experts will be able look at the problem and quickly 
88 88
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
@@ -79,11 +79,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
79 79
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
80 80
 
81 81
 =head2 Support 
82  
- 
  82
+
83 83
 Please direct usage questions or support issues to the mailing list:
84  
-  
85  
-L<bioperl-l@bioperl.org>
86  
-  
  84
+
  85
+I<bioperl-l@bioperl.org>
  86
+
87 87
 rather than to the module maintainer directly. Many experienced and 
88 88
 reponsive experts will be able look at the problem and quickly 
89 89
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Alignment/Probalign.pm
@@ -84,11 +84,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
84 84
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
85 85
 
86 86
 =head2 Support 
87  
- 
  87
+
88 88
 Please direct usage questions or support issues to the mailing list:
89  
-  
90  
-L<bioperl-l@bioperl.org>
91  
-  
  89
+
  90
+I<bioperl-l@bioperl.org>
  91
+
92 92
 rather than to the module maintainer directly. Many experienced and 
93 93
 reponsive experts will be able look at the problem and quickly 
94 94
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Alignment/Probcons.pm
@@ -106,11 +106,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
106 106
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
107 107
 
108 108
 =head2 Support 
109  
- 
  109
+
110 110
 Please direct usage questions or support issues to the mailing list:
111  
-  
112  
-L<bioperl-l@bioperl.org>
113  
-  
  111
+
  112
+I<bioperl-l@bioperl.org>
  113
+
114 114
 rather than to the module maintainer directly. Many experienced and 
115 115
 reponsive experts will be able look at the problem and quickly 
116 116
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Alignment/Proda.pm
@@ -84,11 +84,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
84 84
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
85 85
 
86 86
 =head2 Support 
87  
- 
  87
+
88 88
 Please direct usage questions or support issues to the mailing list:
89  
-  
90  
-L<bioperl-l@bioperl.org>
91  
-  
  89
+
  90
+I<bioperl-l@bioperl.org>
  91
+
92 92
 rather than to the module maintainer directly. Many experienced and 
93 93
 reponsive experts will be able look at the problem and quickly 
94 94
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Alignment/Sim4.pm
@@ -64,11 +64,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
64 64
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
65 65
 
66 66
 =head2 Support 
67  
- 
  67
+
68 68
 Please direct usage questions or support issues to the mailing list:
69  
-  
70  
-L<bioperl-l@bioperl.org>
71  
-  
  69
+
  70
+I<bioperl-l@bioperl.org>
  71
+
72 72
 rather than to the module maintainer directly. Many experienced and 
73 73
 reponsive experts will be able look at the problem and quickly 
74 74
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
@@ -87,11 +87,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
87 87
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
88 88
 
89 89
 =head2 Support 
90  
- 
  90
+
91 91
 Please direct usage questions or support issues to the mailing list:
92  
-  
93  
-L<bioperl-l@bioperl.org>
94  
-  
  92
+
  93
+I<bioperl-l@bioperl.org>
  94
+
95 95
 rather than to the module maintainer directly. Many experienced and 
96 96
 reponsive experts will be able look at the problem and quickly 
97 97
 address it. Please include a thorough description of the problem 
10  lib/Bio/Tools/Run/Alignment/TCoffee.pm
@@ -498,11 +498,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
498 498
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
499 499
 
500 500
 =head2 Support 
501  
- 
  501
+
502 502
 Please direct usage questions or support issues to the mailing list:
503  
-  
504  
-L<bioperl-l@bioperl.org>
505  
-  
  503
+
  504
+I<bioperl-l@bioperl.org>
  505
+
506 506
 rather than to the module maintainer directly. Many experienced and 
507 507
 reponsive experts will be able look at the problem and quickly 
508 508
 address it. Please include a thorough description of the problem 
@@ -768,7 +768,7 @@ sub align {
768 768
            or references to 2 Bio::SimpleAlign objects.
769 769
  Note    : Needs to be updated to run with newer TCoffee code, which
770 770
            allows more than two profile alignments.
771  
-           
  771
+
772 772
 Throws an exception if arguments are not either strings (eg filenames)
773 773
 or references to SimpleAlign objects.
774 774
 
8  lib/Bio/Tools/Run/Analysis.pm
@@ -155,11 +155,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
155 155
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
156 156
 
157 157
 =head2 Support 
158  
- 
  158
+
159 159
 Please direct usage questions or support issues to the mailing list:
160  
-  
161  
-L<bioperl-l@bioperl.org>
162  
-  
  160
+
  161
+I<bioperl-l@bioperl.org>
  162
+
163 163
 rather than to the module maintainer directly. Many experienced and 
164 164
 reponsive experts will be able look at the problem and quickly 
165 165
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Analysis/soap.pm
@@ -43,11 +43,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
43 43
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
44 44
 
45 45
 =head2 Support 
46  
- 
  46
+
47 47
 Please direct usage questions or support issues to the mailing list:
48  
-  
49  
-L<bioperl-l@bioperl.org>
50  
-  
  48
+
  49
+I<bioperl-l@bioperl.org>
  50
+
51 51
 rather than to the module maintainer directly. Many experienced and 
52 52
 reponsive experts will be able look at the problem and quickly 
53 53
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/AnalysisFactory.pm
@@ -91,11 +91,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
91 91
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
92 92
 
93 93
 =head2 Support 
94  
- 
  94
+
95 95
 Please direct usage questions or support issues to the mailing list:
96  
-  
97  
-L<bioperl-l@bioperl.org>
98  
-  
  96
+
  97
+I<bioperl-l@bioperl.org>
  98
+
99 99
 rather than to the module maintainer directly. Many experienced and 
100 100
 reponsive experts will be able look at the problem and quickly 
101 101
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/AnalysisFactory/soap.pm
@@ -40,11 +40,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
40 40
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
41 41
 
42 42
 =head2 Support 
43  
- 
  43
+
44 44
 Please direct usage questions or support issues to the mailing list:
45  
-  
46  
-L<bioperl-l@bioperl.org>
47  
-  
  45
+
  46
+I<bioperl-l@bioperl.org>
  47
+
48 48
 rather than to the module maintainer directly. Many experienced and 
49 49
 reponsive experts will be able look at the problem and quickly 
50 50
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Cap3.pm
@@ -38,11 +38,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
38 38
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
39 39
 
40 40
 =head2 Support 
41  
- 
  41
+
42 42
 Please direct usage questions or support issues to the mailing list:
43  
-  
44  
-L<bioperl-l@bioperl.org>
45  
-  
  43
+
  44
+I<bioperl-l@bioperl.org>
  45
+
46 46
 rather than to the module maintainer directly. Many experienced and 
47 47
 reponsive experts will be able look at the problem and quickly 
48 48
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Coil.pm
@@ -55,11 +55,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
55 55
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
56 56
 
57 57
 =head2 Support 
58  
- 
  58
+
59 59
 Please direct usage questions or support issues to the mailing list:
60  
-  
61  
-L<bioperl-l@bioperl.org>
62  
-  
  60
+
  61
+I<bioperl-l@bioperl.org>
  62
+
63 63
 rather than to the module maintainer directly. Many experienced and 
64 64
 reponsive experts will be able look at the problem and quickly 
65 65
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/EMBOSSApplication.pm
@@ -69,11 +69,11 @@ Bioperl mailing lists  Your participation is much appreciated.
69 69
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
70 70
 
71 71
 =head2 Support 
72  
- 
  72
+
73 73
 Please direct usage questions or support issues to the mailing list:
74  
-  
75  
-L<bioperl-l@bioperl.org>
76  
-  
  74
+
  75
+I<bioperl-l@bioperl.org>
  76
+
77 77
 rather than to the module maintainer directly. Many experienced and 
78 78
 reponsive experts will be able look at the problem and quickly 
79 79
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/EMBOSSacd.pm
@@ -80,11 +80,11 @@ Bioperl mailing lists  Your participation is much appreciated.
80 80
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
81 81
 
82 82
 =head2 Support 
83  
- 
  83
+
84 84
 Please direct usage questions or support issues to the mailing list:
85  
-  
86  
-L<bioperl-l@bioperl.org>
87  
-  
  85
+
  86
+I<bioperl-l@bioperl.org>
  87
+
88 88
 rather than to the module maintainer directly. Many experienced and 
89 89
 reponsive experts will be able look at the problem and quickly 
90 90
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/ERPIN.pm
@@ -75,11 +75,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
75 75
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
76 76
 
77 77
 =head2 Support 
78  
- 
  78
+
79 79
 Please direct usage questions or support issues to the mailing list:
80  
-  
81  
-L<bioperl-l@bioperl.org>
82  
-  
  80
+
  81
+I<bioperl-l@bioperl.org>
  82
+
83 83
 rather than to the module maintainer directly. Many experienced and 
84 84
 reponsive experts will be able look at the problem and quickly 
85 85
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Ensembl.pm
@@ -51,11 +51,11 @@ Bioperl mailing list.  Your participation is much appreciated.
51 51
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
52 52
 
53 53
 =head2 Support 
54  
- 
  54
+
55 55
 Please direct usage questions or support issues to the mailing list:
56  
-  
57  
-L<bioperl-l@bioperl.org>
58  
-  
  56
+
  57
+I<bioperl-l@bioperl.org>
  58
+
59 59
 rather than to the module maintainer directly. Many experienced and 
60 60
 reponsive experts will be able look at the problem and quickly 
61 61
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Eponine.pm
@@ -62,11 +62,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
62 62
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
63 63
 
64 64
 =head2 Support 
65  
- 
  65
+
66 66
 Please direct usage questions or support issues to the mailing list:
67  
-  
68  
-L<bioperl-l@bioperl.org>
69  
-  
  67
+
  68
+I<bioperl-l@bioperl.org>
  69
+
70 70
 rather than to the module maintainer directly. Many experienced and 
71 71
 reponsive experts will be able look at the problem and quickly 
72 72
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/FootPrinter.pm
@@ -134,11 +134,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
134 134
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
135 135
 
136 136
 =head2 Support 
137  
- 
  137
+
138 138
 Please direct usage questions or support issues to the mailing list:
139  
-  
140  
-L<bioperl-l@bioperl.org>
141  
-  
  139
+
  140
+I<bioperl-l@bioperl.org>
  141
+
142 142
 rather than to the module maintainer directly. Many experienced and 
143 143
 reponsive experts will be able look at the problem and quickly 
144 144
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Genemark.pm
@@ -58,11 +58,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
58 58
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
59 59
 
60 60
 =head2 Support 
61  
- 
  61
+
62 62
 Please direct usage questions or support issues to the mailing list:
63  
-  
64  
-L<bioperl-l@bioperl.org>
65  
-  
  63
+
  64
+I<bioperl-l@bioperl.org>
  65
+
66 66
 rather than to the module maintainer directly. Many experienced and 
67 67
 reponsive experts will be able look at the problem and quickly 
68 68
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Genewise.pm
@@ -64,11 +64,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
64 64
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
65 65
 
66 66
 =head2 Support 
67  
- 
  67
+
68 68
 Please direct usage questions or support issues to the mailing list:
69  
-  
70  
-L<bioperl-l@bioperl.org>
71  
-  
  69
+
  70
+I<bioperl-l@bioperl.org>
  71
+
72 72
 rather than to the module maintainer directly. Many experienced and 
73 73
 reponsive experts will be able look at the problem and quickly 
74 74
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Genscan.pm
@@ -44,11 +44,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
44 44
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
45 45
 
46 46
 =head2 Support 
47  
- 
  47
+
48 48
 Please direct usage questions or support issues to the mailing list:
49  
-  
50  
-L<bioperl-l@bioperl.org>
51  
-  
  49
+
  50
+I<bioperl-l@bioperl.org>
  51
+
52 52
 rather than to the module maintainer directly. Many experienced and 
53 53
 reponsive experts will be able look at the problem and quickly 
54 54
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Glimmer.pm
@@ -75,11 +75,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
75 75
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
76 76
 
77 77
 =head2 Support 
78  
- 
  78
+
79 79
 Please direct usage questions or support issues to the mailing list:
80  
-  
81  
-L<bioperl-l@bioperl.org>
82  
-  
  80
+
  81
+I<bioperl-l@bioperl.org>
  82
+
83 83
 rather than to the module maintainer directly. Many experienced and 
84 84
 reponsive experts will be able look at the problem and quickly 
85 85
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Hmmer.pm
@@ -74,11 +74,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
74 74
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
75 75
 
76 76
 =head2 Support 
77  
- 
  77
+
78 78
 Please direct usage questions or support issues to the mailing list:
79  
-  
80  
-L<bioperl-l@bioperl.org>
81  
-  
  79
+
  80
+I<bioperl-l@bioperl.org>
  81
+
82 82
 rather than to the module maintainer directly. Many experienced and 
83 83
 reponsive experts will be able look at the problem and quickly 
84 84
 address it. Please include a thorough description of the problem 
13  lib/Bio/Tools/Run/Infernal.pm
@@ -106,11 +106,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
106 106
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
107 107
 
108 108
 =head2 Support 
109  
- 
  109
+
110 110
 Please direct usage questions or support issues to the mailing list:
111  
-  
112  
-L<bioperl-l@bioperl.org>
113  
-  
  111
+
  112
+I<bioperl-l@bioperl.org>
  113
+
114 114
 rather than to the module maintainer directly. Many experienced and 
115 115
 reponsive experts will be able look at the problem and quickly 
116 116
 address it. Please include a thorough description of the problem 
@@ -685,7 +685,7 @@ sub set_parameters {
685 685
                @_;
686 686
     # set the parameters passed in, but only ones supported for the program
687 687
     my ($prog, $validate) = ($self->program, $self->validate_parameters);
688  
-    
  688
+
689 689
     # parameter cleanup
690 690
     %args = map { my $a = $_;
691 691
               $a =~ s{^-}{};
@@ -856,6 +856,9 @@ sub to_exe_string {
856 856
                                    $self->program_name,
857 857
                                    $self->model_file,
858 858
                                    $self->outfile_name);
  859
+    
  860
+    $self->throw("Executable not found") unless defined($exe);
  861
+    
859 862
     delete $params{o} if exists $params{o};
860 863
 
861 864
     if (!defined($model) && $prog ne 'cmbuild') {
8  lib/Bio/Tools/Run/MCS.pm
@@ -94,11 +94,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
94 94
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
95 95
 
96 96
 =head2 Support 
97  
- 
  97
+
98 98
 Please direct usage questions or support issues to the mailing list:
99  
-  
100  
-L<bioperl-l@bioperl.org>
101  
-  
  99
+
  100
+I<bioperl-l@bioperl.org>
  101
+
102 102
 rather than to the module maintainer directly. Many experienced and 
103 103
 reponsive experts will be able look at the problem and quickly 
104 104
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Match.pm
@@ -79,11 +79,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
79 79
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
80 80
 
81 81
 =head2 Support 
82  
- 
  82
+
83 83
 Please direct usage questions or support issues to the mailing list:
84  
-  
85  
-L<bioperl-l@bioperl.org>
86  
-  
  84
+
  85
+I<bioperl-l@bioperl.org>
  86
+
87 87
 rather than to the module maintainer directly. Many experienced and 
88 88
 reponsive experts will be able look at the problem and quickly 
89 89
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Mdust.pm
@@ -58,11 +58,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
58 58
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
59 59
 
60 60
 =head2 Support 
61  
- 
  61
+
62 62
 Please direct usage questions or support issues to the mailing list:
63  
-  
64  
-L<bioperl-l@bioperl.org>
65  
-  
  63
+
  64
+I<bioperl-l@bioperl.org>
  65
+
66 66
 rather than to the module maintainer directly. Many experienced and 
67 67
 reponsive experts will be able look at the problem and quickly 
68 68
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Meme.pm
@@ -57,11 +57,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
57 57
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
58 58
 
59 59
 =head2 Support 
60  
- 
  60
+
61 61
 Please direct usage questions or support issues to the mailing list:
62  
-  
63  
-L<bioperl-l@bioperl.org>
64  
-  
  62
+
  63
+I<bioperl-l@bioperl.org>
  64
+
65 65
 rather than to the module maintainer directly. Many experienced and 
66 66
 reponsive experts will be able look at the problem and quickly 
67 67
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Phrap.pm
@@ -52,11 +52,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
52 52
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
53 53
 
54 54
 =head2 Support 
55  
- 
  55
+
56 56
 Please direct usage questions or support issues to the mailing list:
57  
-  
58  
-L<bioperl-l@bioperl.org>
59  
-  
  57
+
  58
+I<bioperl-l@bioperl.org>
  59
+
60 60
 rather than to the module maintainer directly. Many experienced and 
61 61
 reponsive experts will be able look at the problem and quickly 
62 62
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Phylo/Gerp.pm
@@ -87,11 +87,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
87 87
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
88 88
 
89 89
 =head2 Support 
90  
- 
  90
+
91 91
 Please direct usage questions or support issues to the mailing list:
92  
-  
93  
-L<bioperl-l@bioperl.org>
94  
-  
  92
+
  93
+I<bioperl-l@bioperl.org>
  94
+
95 95
 rather than to the module maintainer directly. Many experienced and 
96 96
 reponsive experts will be able look at the problem and quickly 
97 97
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Phylo/Gumby.pm
@@ -103,11 +103,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
103 103
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
104 104
 
105 105
 =head2 Support 
106  
- 
  106
+
107 107
 Please direct usage questions or support issues to the mailing list:
108  
-  
109  
-L<bioperl-l@bioperl.org>
110  
-  
  108
+
  109
+I<bioperl-l@bioperl.org>
  110
+
111 111
 rather than to the module maintainer directly. Many experienced and 
112 112
 reponsive experts will be able look at the problem and quickly 
113 113
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Phylo/Hyphy/Base.pm
@@ -38,11 +38,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
38 38
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
39 39
 
40 40
 =head2 Support 
41  
- 
  41
+
42 42
 Please direct usage questions or support issues to the mailing list:
43  
-  
44  
-L<bioperl-l@bioperl.org>
45  
-  
  43
+
  44
+I<bioperl-l@bioperl.org>
  45
+
46 46
 rather than to the module maintainer directly. Many experienced and 
47 47
 reponsive experts will be able look at the problem and quickly 
48 48
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
@@ -57,11 +57,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
57 57
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
58 58
 
59 59
 =head2 Support 
60  
- 
  60
+
61 61
 Please direct usage questions or support issues to the mailing list:
62  
-  
63  
-L<bioperl-l@bioperl.org>
64  
-  
  62
+
  63
+I<bioperl-l@bioperl.org>
  64
+
65 65
 rather than to the module maintainer directly. Many experienced and 
66 66
 reponsive experts will be able look at the problem and quickly 
67 67
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
@@ -56,11 +56,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
56 56
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
57 57
 
58 58
 =head2 Support 
59  
- 
  59
+
60 60
 Please direct usage questions or support issues to the mailing list:
61  
-  
62  
-L<bioperl-l@bioperl.org>
63  
-  
  61
+
  62
+I<bioperl-l@bioperl.org>
  63
+
64 64
 rather than to the module maintainer directly. Many experienced and 
65 65
 reponsive experts will be able look at the problem and quickly 
66 66
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Phylo/Hyphy/REL.pm
@@ -57,11 +57,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
57 57
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
58 58
 
59 59
 =head2 Support 
60  
- 
  60
+
61 61
 Please direct usage questions or support issues to the mailing list:
62  
-  
63  
-L<bioperl-l@bioperl.org>
64  
-  
  62
+
  63
+I<bioperl-l@bioperl.org>
  64
+
65 65
 rather than to the module maintainer directly. Many experienced and 
66 66
 reponsive experts will be able look at the problem and quickly 
67 67
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
@@ -55,11 +55,11 @@ the Bioperl mailing list.  Your participation is much appreciated.
55 55
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
56 56
 
57 57
 =head2 Support 
58  
- 
  58
+
59 59
 Please direct usage questions or support issues to the mailing list:
60  
-  
61  
-L<bioperl-l@bioperl.org>
62  
-  
  60
+
  61
+I<bioperl-l@bioperl.org>
  62
+
63 63
 rather than to the module maintainer directly. Many experienced and 
64 64
 reponsive experts will be able look at the problem and quickly 
65 65
 address it. Please include a thorough description of the problem 
8  lib/Bio/Tools/Run/Phylo/LVB.pm
@@ -56,11 +56,11 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
56 56
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
57 57
 
58 58
 =head2 Support 
59  
- 
  59
+
60 60
 Please direct usage questions or support issues to the mailing list:
61  
-  
62  
-L<bioperl-l@bioperl.org>
63  
-  
  61
+
  62
+I<bioperl-l@bioperl.org>
  63
+
64 64
 rather than to the module maintainer directly. Many experienced and 
65 65