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diff --git a/academic/treebest-ensembl/README b/academic/treebest-ensembl/README new file mode 100644 index 0000000000000..b6639d304d237 --- /dev/null +++ b/academic/treebest-ensembl/README @@ -0,0 +1,29 @@ +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. |