treebest

TreeBeST: Tree Building guided by Species Tree (Ensembl Compara modifications)

This repository holds the necessary changes of Heng Li's version to run the latest Ensembl Compara pipeline.

You can find more documentation on SourceForge: (http://treesoft.sourceforge.net/treebest.shtml)

The main new features are:

• new -s option in treebest sdi, to allow a user-defined species tree. This change is from Albert Vilella
• new T node-tag in the NHX output: a bit-field listing the input trees that support the node. This is populated by the mmerge algorithm
• new -I option in treebest nj, to carry on the T tags from the input tree
• new -Z option in treebest best, to redefine the PhyML variable MIN_DIFF_LK. It prevents PhyML from crashing during its computation
• new -X option in treebest best, to give a higher weight to the likelihood that comes from the reconciliation with the species tree (default 1)
• 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.
• new -I option in treebest best, to start from the input tree instead of building one

Other changes include:

• bugfixes / tweaks when processing the filtered alignments (TreeBeST includes a Clustal-score-based MSA-filtering step)
• bugfixes / tweaks when merging the trees
• using double instead of float for floating-point values

Branches and tags

There is a single branch (master) where all the development goes. The version number stated in the source code (1.9.2) is not maintained.

Tags are used to point at specific versions:

• lh3: when Heng Li handed-over the code to Ensembl Compara
• albert: changes made by Albert Vilella
• ensembl_production_XX: the version used for the production of Ensembl version XX