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BUG FIX: this fixes a long-standing bug that was just discovered. Pre…
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…vious

versions of the code used 'centroid' breaking even if the user specified
break_strategy  = longest

The resulting alignment and tree estimates should still be conform to valid
estimates using SATe with centroid edge-breaking strategy.

This bug dates back to commit 83c669b473282ffa191ee37acd868a69f32413c1
on the old sate repo ( https://github.com/jiaye/msaml ). This is version 1.0
and the commit date is March 17, 2010. So this bug effects all versions of SATe
that have been posted on the binary website.
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@mtholder
mtholder committed May 12, 2012
1 parent d13f5b5 commit 7159a21
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion sate/satealignerjob.py
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Expand Up @@ -293,7 +293,7 @@ def wait(self):
def bipartition_by_tree(self, option):
_LOG.debug("tree before bipartition by %s = %s" % (option, self.tree.compose_newick()))

tree1, tree2 = bisect_tree(self.tree)
tree1, tree2 = bisect_tree(self.tree, breaking_edge_style=option)
assert tree1.n_leaves > 0
assert tree2.n_leaves > 0
assert tree1.n_leaves + tree2.n_leaves == self.tree.n_leaves
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Github seems to be assuming the SHA in the commit message refers to this repo (which is usually the case). The commit is actually https://github.com/jiaye/msaml/commit/83c669b473282ffa191ee37acd868a69f32413c1

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