Changelog

Additions

• New alignment color schemes
  • Color schemes for protein sequence alignments created with Gecos software
    • Including a color scheme adapted for red-green blindness
  • Color scheme for protein block sequence alignments created with Gecos software
  • Color schemes for protein sequence alignments adapted from JalView
• More functionalities for external MSA software (application.MSAApp subclasses)
  • Additional CLI options can be set via add_additional_options()
  • The executed command of application.LocalApp can be optained via get_coomand()
  • Most MSA software interfaces allow setting and getting the distance matrix and the guide tree
    • The corresponding method are get_guide_tree(), set_guide_tree(), get_distance_matrix() and set_distance_matrix()
  • MSA software supporting cutom substitution matrices can be used to align almost any type of sequence, even if the type is not directly supported by the underlying software
• Added euality operator for sequence.align.Alignment objects
• sequence.phylo.Tree supports non-binary trees
  • sequence.phylo.TreeNode can handle more than two child nodes
  • len() gives amount of leaves in sequence.phylo.Tree
  • sequence.phylo.Tree and sequence.phylo.TreeNode support hash and equality operator
  • sequence.phylo.as_binary() function converts non-binary tree into binary tree, as required for guide trees
• Added sequence.phylo.neighbor_joining() for hierarchical clustering

Changes

• Removed X as symbol for ambiguous nucleotides, use N instead
• Removed protected method get_default_bin_path() from application.MSAApp
• Renamed protected method set_options() to set_arguments() application.LocalApp
• Renamed set_matrix() to set_substitution_matrix() application.muscle.MuscleApp
• Removed protected method get_cli_arguments() in application.LocalApp
• Adapted constructor of sequence.phylo.TreeNode for variable amount of child nodes
• application.MSAApp subclasses must implement abstract static methods describing which sequence types they support and whether they support custom substitution matrices

Fixes

• U is automatically converted to T when loading nulceotide sequences from FASTA files
• Score matrix in sequence.align.SubstitutionMatrix is now truly read-only via ndarray flag
• application.Application subclasses (all external software interfaces) now properly check whether the corresponding objects are in the correct application.AppState
• Error in evaluation step of application.Application now leaves application in application.AppState.CANCELLED state
• Fixed InvalidFileError not being exposed to user
• Symmetry checks in sequence.phylo.upgma() allow for small rounding errors