path: root/academic/treebest-ensembl/README

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.