Table of Contents - bio-alignment-0.1.0 Documentation
Pages
Classes and Modules
- Bio
- Bio::BioAlignment
- Bio::BioAlignment::Alignment
- Bio::BioAlignment::Codon
- Bio::BioAlignment::CodonSequence
- Bio::BioAlignment::Coerce
- Bio::BioAlignment::Column
- Bio::BioAlignment::ColumnState
- Bio::BioAlignment::Columns
- Bio::BioAlignment::DelBridges
- Bio::BioAlignment::DelNonInformativeSequences
- Bio::BioAlignment::DelShortSequences
- Bio::BioAlignment::DeleteState
- Bio::BioAlignment::Element
- Bio::BioAlignment::ElementMaskedState
- Bio::BioAlignment::ElementState
- Bio::BioAlignment::Elements
- Bio::BioAlignment::FastaOutput
- Bio::BioAlignment::MarkColumns
- Bio::BioAlignment::MarkRows
- Bio::BioAlignment::MarkState
- Bio::BioAlignment::MaskIslands
- Bio::BioAlignment::MaskIslands::IslandElementState
- Bio::BioAlignment::MaskSerialMutations
- Bio::BioAlignment::MaskState
- Bio::BioAlignment::Pal2Nal
- Bio::BioAlignment::PhylipOutput
- Bio::BioAlignment::Row
- Bio::BioAlignment::RowState
- Bio::BioAlignment::Rows
- Bio::BioAlignment::Sequence
- Bio::BioAlignment::State
- Bio::BioAlignment::TextOutput
- Bio::BioAlignment::Tree
- Bio::BioAlignment::Tree::Node
- Bio::BioAlignment::TreeSplitter
- Bio::Sequence
- Bio::Sequence::AA
- Bio::Sequence::NA
- Bio::Tree
- Bio::Tree::Node
Methods
- ::fetch_id — Bio::BioAlignment::Coerce
- ::fetch_seq — Bio::BioAlignment::Coerce
- ::fetch_seq_string — Bio::BioAlignment::Coerce
- ::header — Bio::BioAlignment::PhylipOutput
- ::init — Bio::BioAlignment::Tree
- ::new — Bio::BioAlignment::Alignment
- ::new — Bio::BioAlignment::Codon
- ::new — Bio::BioAlignment::CodonSequence
- ::new — Bio::BioAlignment::Column
- ::new — Bio::BioAlignment::Element
- ::new — Bio::BioAlignment::Elements
- ::new — Bio::BioAlignment::Row
- ::new — Bio::BioAlignment::Sequence
- ::to_elements — Bio::BioAlignment::Coerce
- ::to_fasta — Bio::BioAlignment::FastaOutput
- ::to_paml — Bio::BioAlignment::PhylipOutput
- ::to_text — Bio::BioAlignment::TextOutput
- #<< — Bio::BioAlignment::Alignment
- #<< — Bio::BioAlignment::CodonSequence
- #<< — Bio::BioAlignment::Elements
- #<< — Bio::BioAlignment::Sequence
- #== — Bio::BioAlignment::Codon
- #== — Bio::BioAlignment::Element
- #[] — Bio::BioAlignment::Alignment
- #[] — Bio::BioAlignment::CodonSequence
- #[] — Bio::BioAlignment::Column
- #[] — Bio::BioAlignment::Elements
- #[] — Bio::BioAlignment::Sequence
- #alignment — Bio::Tree::Node
- #attach_tree — Bio::BioAlignment::Alignment
- #children — Bio::Tree::Node
- #clone — Bio::BioAlignment::Alignment
- #clone — Bio::BioAlignment::Element
- #clone — Bio::BioAlignment::Elements
- #clone — Bio::BioAlignment::Sequence
- #clone — Bio::Tree
- #clone_columns! — Bio::BioAlignment::Columns
- #clone_subtree — Bio::Tree
- #clone_tree_without_branch — Bio::Tree
- #columns — Bio::BioAlignment::Columns
- #columns_to_s — Bio::BioAlignment::Columns
- #columns_where — Bio::BioAlignment::Columns
- #count — Bio::BioAlignment::Column
- #count — Bio::BioAlignment::Row
- #del_bridges — Bio::BioAlignment::DelBridges
- #del_non_informative_sequences — Bio::BioAlignment::DelNonInformativeSequences
- #del_short_sequences — Bio::BioAlignment::DelShortSequences
- #delete! — Bio::BioAlignment::DeleteState
- #deleted? — Bio::BioAlignment::DeleteState
- #descendents — Bio::Tree::Node
- #distance — Bio::Tree::Node
- #each — Bio::BioAlignment::Alignment
- #each — Bio::Sequence::NA
- #each — Bio::Sequence::AA
- #each — Bio::BioAlignment::CodonSequence
- #each — Bio::BioAlignment::Column
- #each — Bio::BioAlignment::Elements
- #each — Bio::BioAlignment::Sequence
- #each_element — Bio::BioAlignment::Alignment
- #empty_copy — Bio::BioAlignment::CodonSequence
- #empty_copy — Bio::BioAlignment::Elements
- #empty_copy — Bio::BioAlignment::Sequence
- #find — Bio::BioAlignment::Alignment
- #find — Bio::Tree
- #gap? — Bio::BioAlignment::Codon
- #gap? — Bio::BioAlignment::Element
- #ids — Bio::BioAlignment::Alignment
- #inject_tree — Bio::Tree::Node
- #leaf? — Bio::Tree::Node
- #leaves — Bio::Tree::Node
- #length — Bio::BioAlignment::CodonSequence
- #length — Bio::BioAlignment::Column
- #length — Bio::BioAlignment::Elements
- #length — Bio::BioAlignment::Sequence
- #map — Bio::Tree
- #mark! — Bio::BioAlignment::MarkState
- #mark_bridges — Bio::BioAlignment::DelBridges
- #mark_columns — Bio::BioAlignment::MarkColumns
- #mark_island — Bio::BioAlignment::MaskIslands
- #mark_islands — Bio::BioAlignment::MaskIslands
- #mark_non_informative_sequences — Bio::BioAlignment::DelNonInformativeSequences
- #mark_row_elements — Bio::BioAlignment::MarkRows
- #mark_rows — Bio::BioAlignment::MarkRows
- #mark_serial_mutations — Bio::BioAlignment::MaskSerialMutations
- #mark_short_sequences — Bio::BioAlignment::DelShortSequences
- #marked? — Bio::BioAlignment::MarkState
- #markrows_clone — Bio::BioAlignment::MarkRows
- #mask! — Bio::BioAlignment::MaskState
- #masked? — Bio::BioAlignment::MaskState
- #nearest — Bio::Tree::Node
- #nearest_child — Bio::Tree::Node
- #nearest_children — Bio::Tree::Node
- #num_columns — Bio::BioAlignment::Columns
- #pal2nal — Bio::BioAlignment::Pal2Nal
- #parent — Bio::Tree::Node
- #print_island — Bio::BioAlignment::MaskIslands
- #root — Bio::BioAlignment::Tree
- #rows_where — Bio::BioAlignment::Rows
- #sequence — Bio::Tree::Node
- #siblings — Bio::Tree::Node
- #size — Bio::BioAlignment::Alignment
- #split_on_distance — Bio::BioAlignment::TreeSplitter
- #to_aa — Bio::BioAlignment::Codon
- #to_aa — Bio::BioAlignment::CodonSequence
- #to_bioruby_alignment — Bio::BioAlignment::Alignment
- #to_elements — Bio::BioAlignment::CodonSequence
- #to_elements — Bio::BioAlignment::Sequence
- #to_nt — Bio::BioAlignment::CodonSequence
- #to_s — Bio::BioAlignment::Alignment
- #to_s — Bio::BioAlignment::Codon
- #to_s — Bio::BioAlignment::CodonSequence
- #to_s — Bio::BioAlignment::Column
- #to_s — Bio::BioAlignment::MaskIslands::IslandElementState
- #to_s — Bio::BioAlignment::Element
- #to_s — Bio::BioAlignment::Elements
- #to_s — Bio::BioAlignment::Sequence
- #to_s — Bio::BioAlignment::DeleteState
- #to_s — Bio::BioAlignment::MarkState
- #to_s — Bio::BioAlignment::MaskState
- #translate — Bio::BioAlignment::Codon
- #tree_reduce — Bio::BioAlignment::Alignment
- #undefined? — Bio::BioAlignment::Codon
- #undefined? — Bio::BioAlignment::Element
- #unmark! — Bio::BioAlignment::MarkState
- #unmask! — Bio::BioAlignment::MaskState
- #update_each_element — Bio::BioAlignment::Alignment