Lots of bug fixes. For example the Bio::Fasta.remote bug has been fixed, workaround for Zlib error, fixed method names
Increased ruby 1.9 support
Renaming of files and modules
Some files and modules have been renamed for example Bio::Fastq:QualityScore has been renamed to Bio::Sequence::QualityScore
There is a samples folder that include sample usage of some classes and methods
Support for the phyloxml parser and writer has been included. A new version(1.10) of the PhyloXML schema has been added.
This contribution was provided by the awesome Latvian girl through a Google Summer of Code project and working for NESCent organization.
Meme and Mast support
Contributed by Adam Kraut. Minimal and basic support for the motif finding application Meme and Mast has been added.
Speed up of Bio::Tree.children
* Bio::Tree#parent is changed to directly raise IndexError when
* Bio::Tree#path is changed not to call bfs_shortest_path if the
"lib/bio/db/fasta/fasta_to_biosequence.rb", "lib/bio/db/fastq/fastq_to_biosequence.rb", "lib/bio/db/fastq/format_fastq.rb", "lib/bio/db/fastq.rb", "lib/bio/db/sanger_chromatogram/abif.rb", "lib/bio/db/sanger_chromatogram/chromatogram.rb", "lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb", "lib/bio/db/sanger_chromatogram/scf.rb", "lib/bio/db/phyloxml/phyloxml.xsd", "lib/bio/db/phyloxml/phyloxml_elements.rb", "lib/bio/db/phyloxml/phyloxml_parser.rb", "lib/bio/db/phyloxml/phyloxml_writer.rb", "lib/bio/sequence/quality_score.rb"