Changelog

Additions

• Added support for phylogenetic trees
  • Represented by sequence.phylo.Tree and sequence.phylo.TreeNode class
  • Can be read from/ written into Newick format
  • sequence.phylo.upgma() for sequence.phylo.Tree creation from distances
• Added sequence.align.align_multiple() for simple multiple sequence alignments
• Added customization methods in application.muscle.MuscleApp
• Revamped visualiazation system
  • Usage of functions instead of Visualizer objects
  • sequence.graphics.SymbolPlotter class for custom alignment visualizations
  • sequence.graphics.FeaturePlotter class for custom feature visualizations
• Added sequence.graphics.plot_dendrogram() for sequence.phylo.Tree visualization
• Expanded the tutorial

Changes

• Revamped visualization system (see Additions)

Fixes

• Added max_number parameter in sequence.align.align_optimal() to avoid branch explosion
• Fixed rare scoring error in sequence.align.align_optimal()
• Fixed slicing sequence.Annotation objects with multi-location features