What’s new in ETE 2.2

BUGFIXES

SCRIPTS

  • Improvements in the standalone visualization script (a.k.a. ete2)
  • Added the etree2orthoxml script, which provides conversion between phylogenetic tree and the orthoXML format

NEW MODULES

NEW FEATURES

  • News in core Tree instances:

    • Added TreeNode.robinson_foulds() distance to compare the topology of two trees (i.e. tree.robinson_foulds(tree2)). It includes automatic pruning to compare trees of different sizes. See tutorial and examples

    • Added new options to TreeNode.copy() function, allowing faster methods to duplicate tree node instances. See tutorial and examples

    • Added preserve_branch_length argument to TreeNode.prune() and TreeNode.delete(), which allows to remove nodes from a tree while keeping original branch length distances among the remaining nodes.

    • Added TreeNode.resolve_polytomy() function to convert multifurcated nodes into an arbitrary structure of binary split nodes with distance. See tutorial and examples

    • Added TreeNode.get_cached_content() function, which returns a dictionary linking each node instance with its leaf content. Such a dictionary might be used as a cache to speed up functions that require intensive use of node traversing. See tutorial and examples

    • Improved TreeNode.get_ascii() function for text-based visualization of trees. A new attributes argument can be passed to display node attributes within the ASCII tree representation.

      from ete2 import Tree
t = Tree("((A, B)Internal_1:0.7, (C, D)Internal_2:0.5)root:1.3;", format=1)
t.add_features(size=4)
print t.get_ascii(attributes=["name", "dist", "size"])
#
#                            /-A, 0.0
#             /Internal_1, 0.7
#            |               \-B, 0.0
# -root, 1.3, 4
#            |               /-C, 0.0
#             \Internal_2, 0.5
#                            \-D, 0.0
#

    • Random branch length and support values generation is now available for the TreeNode.populate() function.

    • a new argument is_leaf_fn is available for a number of traversing functions, thus allowing to provide custom stopping criteria when browsing a tree. This is, any node matching the function provided through the is_leaf_fn argument will be temporarily considered as a terminal/leaf node by the traversing function (tree will look as a pruned version of itself). See tutorial and examples

    • Added TreeNode.iter_ancestors() and TreeNode.get_ancestors() functions.

    • Added TreeNode.iter_prepostorder() tree node iterator.

    • Newick parser accepts now the creation of single node trees. For example, a text string such as "node1;" will be parsed as a single tree node whose name is node1. By contrast, the newick string (node1); will be interpreted as an unnamed root node plus a single child named name1.

    • TreeNode.write() accepts now a format_root_node argument to export root node features as a part of the newick string.

    • The new TreeNode.check_monophyly() method allows to check if a node is mono, poly or paraphyletic for a given attribute and values (i.e. grouped species). Although monophyly is actually a phylogenetic concept, the idea can be applied to any tree, so any topology could be queried for the monophyly of certain attribute values. If not monophyletic, the method will return also the type of relationship connecting the provided values (para- or poly-phyletic). See tutorial and examples

    • New TreeNode.get_monophyletic() method that returns a list of nodes in a tree matching a custom monophyly criteria.

  • News PhyloTree instances:

  • News on sequence and multiple sequence alignment parsing:

    • added the option to disable the automatic correction of duplicated names when loading SeqGroup data from phylip and fasta files.

  • News on tree visualization and image rendering:

    • node style attributes can now be modified without the need of initialization by directly accessing the TreeNode.img_style attribute.

    • Multiple layout functions can now be provided to combine their functionality. This way, you can keep separate styling templates and combine them as necessary.

      from ete2 import TreeStyle

def color_leaves(node):
    if node.is_leaf():
       node.img_style["fgcolor"] = "red"

def size_internal(node):
    if not node.is_leaf():
       node.img_style["size"] = 15

ts = TreeStyle()
# provide a list of layout functions, instead of a single one
ts.layout_fn = [color_leaves, size_internal]

    • COLOR_SCHEMES and SVG_COLORS dictionaries are provided for easy access to color codes and several predefined color schemes. In addition, a random_color() function is also available as a generator of RGB colors (where saturation and lightness can be fixed).

      from ete2 import random_color, COLOR_SCHEMES, SVG_COLORS

# generate 20 random colors
node_colors = [random_color(s=0.4, l=4) for i in xrange(20)]

  • News on node faces:

    • New face.rotation attribute, that allows to rotate individual faces even when a global treestyle.rotation is used.

      ../_images/rotated_faces.png

    • Improved SequenceFace: Sequence sites are now rendered one by one, allowing interaction with each of them and getting rid of the previous pixmap size limitation. Site image dimensions and colours are now configurable.

    • Added new SeqMotifFace class, which represent an enriched version of the former SequenceFace instance. This new face type allows to represent sequences as a succession of domain/motif elements or to represent sequence positions as color points. Gaps can also be taken into account and therefore shown as as a black space or a flat line.

      ../_images/seqmotif.png

    • Added PieChartFace and BarChartFace face types for built-in representation of statistics attached to nodes.

      ../_images/float_piechart.png
      ../_images/barcharts.png

    • Improved ImgFace class, now accepting on the fly image scaling.

  • News on the GUI

    • Allows image region selection.
    • Allows zooming on selected regions or specific nodes (Z - zoomIn, X - zoomOut, R - focus region).
    • C-c will now interrupt the GUI application when started from a terminal.
    • Added keyboard-based node navigation (click on a node and play the arrow keys).