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Commits on Jun 25, 2012
  1. Include BGZF examples

    peterjc committed Jun 25, 2012
Commits on Jun 24, 2012
  1. Phylo: fixed the bug in root_at_midpoint

    etal committed Jun 24, 2012
    Most trees don't have a branch length assigned to the root, so depths()
    was ignoring this value without a noticeable problem. But when
    root_at_midpoint() calls depths() on child clades, the leading branch
    length should be included, at it wasn't.
    
    Solution: include the root branch length in depths(). In
    root_at_midpoint(), adjust the calculation of 'remainder' for the root
    branch length since the root branch will not be traversed.
  2. Phylo.draw: make x-margins more robust/reliable

    etal committed Jun 24, 2012
    Take xmax from the calculated taxon positions, rather than matplotlib's first
    guess at the x-axis limits; base the margin calculations on that value, so that
    taxon labels are less likely to overflow the plot.
  3. Phylo.draw: show integer confidences with no decimal

    etal committed Jun 24, 2012
    e.g. show 100.0 as "100", by default.
Commits on Jun 23, 2012
Commits on Jun 22, 2012
  1. Fix example under Python 2.5

    peterjc committed Jun 22, 2012
  2. Update test file readme file

    peterjc committed Jun 22, 2012
Commits on Jun 21, 2012
  1. BGZF docstring tidying

    peterjc committed Apr 17, 2012
  2. Minor docstring clarification

    peterjc committed Apr 17, 2012
  3. Revert "Record compression type in SeqIO.index_db()"

    peterjc committed Mar 19, 2012
    This reverts commit 6ab5e8911186a39392247ab7a31abb10ed2ac288.