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academic/treebest-ensembl: Wrap README at 72 columns.

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Signed-off-by: B. Watson <yalhcru@gmail.com>
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B. Watson 2022-03-12 14:40:15 -05:00
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academic/treebest-ensembl/README
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@ -10,16 +10,18 @@ TreeBeST is previously known as NJTREE. It has been largely used in the
TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting
group.
This is the Ensembl Compara modifications version. The main new features
are:
This is the Ensembl Compara modifications version. The main new
features are:
1) -s option in treebest sdi, to allow a user-defined species tree.
T node-tag in the NHX output: a bit-field listing the input trees
2) that support the node.
3) -I option in treebest nj, to carry on the T tags from the input tree
4) -Z option in treebest best, to redefine the PhyML variable MIN_DIFF_LK
5) -X option in treebest best, to give a higher weight to the likelihood
that comes from the reconciliation with the species tree (default 1)
4) -Z option in treebest best, to redefine the PhyML variable
MIN_DIFF_LK
5) -X option in treebest best, to give a higher weight to the
likelihood that comes from the reconciliation with the species tree
(default 1)
6) -I option in treebest best, to start from the input tree instead of
building one
7) Species-intersection scores are now also reported as floating-point