academic/treebest-ensembl: Added (Tree Building).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

1 files changed, 29 insertions, 0 deletions

diff --git a/academic/treebest-ensembl/README b/academic/treebest-ensembl/README
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+TreeBeST: Tree Building guided by Species Tree
+(Ensembl Compara modifications)
+
+TreeBeST, which stands for (gene) Tree Building guided by Species Tree,
+is a versatile program that builds, manipulates and displays
+phylogenetic trees. It is particularly designed for building gene trees
+with a known species tree and is highly efficient and accurate.
+
+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:
+
+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)
+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
+    values under the DCS node-tag. The value is between 0 and 1, and
+    displayed with 4 decimals.
+
+The script builds both the command line and GUI versions of treebest.