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Biotite 0.16.0

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@padix-key padix-key released this 16 Aug 13:31
bed7b6d

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