From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: Debian "lintian" inspired spelling fixes
--- bioperl.orig/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm
+++ bioperl/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm
@@ -469,7 +469,7 @@
 boolean flag: it must be present and set to 0 for the data to be tagged for
 Bio::LocatableSeq or similar (in all other cases it is assumed to be for the
 alignment). In some cases this will not matter (the actual sequence data, for
-instance) but it is highly recommmended adding this tag in to prevent possible
+instance) but it is highly recommended adding this tag in to prevent possible
 ambiguities.
 
 This is the current Annotation data chunk (via Data::Dumper):
--- bioperl.orig/lib/Bio/Index/EMBL.pm
+++ bioperl/lib/Bio/Index/EMBL.pm
@@ -48,7 +48,7 @@
 =head1 DESCRIPTION
 
 Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
-and provides the basic funtionallity for indexing EMBL files, and
+and provides the basic funtionality for indexing EMBL files, and
 retrieving the sequence from them. Heavily snaffled from James Gilbert
 and his Fasta system. Note: for best results 'use strict'.
 
--- bioperl.orig/lib/Bio/Index/Fasta.pm
+++ bioperl/lib/Bio/Index/Fasta.pm
@@ -48,7 +48,7 @@
 =head1 DESCRIPTION
 
 Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
-and provides the basic funtionallity for indexing fasta files, and
+and provides the basic funtionality for indexing fasta files, and
 retrieving the sequence from them. For best results 'use strict'.
 
 Bio::Index::Fasta supports the Bio::DB::BioSeqI interface, meaning
--- bioperl.orig/lib/Bio/Index/Fastq.pm
+++ bioperl/lib/Bio/Index/Fastq.pm
@@ -46,7 +46,7 @@
 =head1 DESCRIPTION
 
 Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
-and provides the basic funtionallity for indexing fastq files, and
+and provides the basic funtionality for indexing fastq files, and
 retrieving the sequence from them. Note: for best results 'use strict'.
 
 Bio::Index::Fastq supports the Bio::DB::BioSeqI interface, meaning
--- bioperl.orig/lib/Bio/Index/Qual.pm
+++ bioperl/lib/Bio/Index/Qual.pm
@@ -46,7 +46,7 @@
 =head1 DESCRIPTION
 
 Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
-and provides the basic funtionallity for indexing qual files, and
+and provides the basic funtionality for indexing qual files, and
 retrieving the sequence from them. For best results 'use strict'.
 
 Bio::Index::Qual supports the Bio::DB::BioSeqI interface, meaning
--- bioperl.orig/lib/Bio/Index/SwissPfam.pm
+++ bioperl/lib/Bio/Index/SwissPfam.pm
@@ -45,7 +45,7 @@
 provides a way of indexing this module.
 
 Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and 
-provides the basic funtionallity for indexing SwissPfam files.  Only 
+provides the basic funtionality for indexing SwissPfam files.  Only 
 retrieves FileStreams at the moment. Once we have something better 
 (ie, an object!), will use that. Heavily snaffled from Index::Fasta system of 
 James Gilbert. Note: for best results 'use strict'.
--- bioperl.orig/lib/Bio/Tools/Run/Analysis.pm
+++ bioperl/lib/Bio/Tools/Run/Analysis.pm
@@ -776,7 +776,7 @@
 
 It makes an expert guess what kind of access/transport protocol should
 be used to access the underlying analysis. The guess is based on the
-parameters in I<rh_params>. Rememeber that this method is called only
+parameters in I<rh_params>. Remember that this method is called only
 if there was no I<-access> parameter which could tell directly what
 access method to use.
 
--- bioperl.orig/lib/Bio/Tools/Run/AnalysisFactory.pm
+++ bioperl/lib/Bio/Tools/Run/AnalysisFactory.pm
@@ -336,7 +336,7 @@
 
 It makes an expert guess what kind of access/transport protocol should
 be used to access the underlying analysis. The guess is based on the
-parameters in I<rh_params>. Rememeber that this method is called only
+parameters in I<rh_params>. Remember that this method is called only
 if there was no I<-access> parameter which could tell directly what
 access method to use.
 
--- bioperl.orig/lib/Bio/Tools/TandemRepeatsFinder.pm
+++ bioperl/lib/Bio/Tools/TandemRepeatsFinder.pm
@@ -26,7 +26,7 @@
 Written and tested for version 4.00
 
 Location, seq_id, and score are stored in Bio::SeqFeature::Generic feature.
-All other data is stored in tags.  The availabale tags are
+All other data is stored in tags.  The available tags are
 
         period_size
         copy_number
--- bioperl.orig/lib/Bio/Tree/Statistics.pm
+++ bioperl/lib/Bio/Tree/Statistics.pm
@@ -673,7 +673,7 @@
 
   Example    : phylotype_length($tree, $node);
   Description: Sums up the branch lengths within phylotype
-               exluding the subclusters where the trait values
+               excluding the subclusters where the trait values
                are different
   Returns    : float, length
   Exceptions : all the  nodes need to have the trait defined
@@ -723,7 +723,7 @@
 
   Example    : sum_of_leaf_distances($tree, $node);
   Description: Sums up the branch lengths from root to leaf
-               exluding the subclusters where the trait values
+               excluding the subclusters where the trait values
                are different
   Returns    : float, length
   Exceptions : all the  nodes need to have the trait defined
