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31 lines
1.3 KiB
Text
31 lines
1.3 KiB
Text
TreeBeST: Tree Building guided by Species Tree
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(Ensembl Compara modifications)
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TreeBeST, which stands for (gene) Tree Building guided by Species Tree,
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is a versatile program that builds, manipulates and displays
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phylogenetic trees. It is particularly designed for building gene trees
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with a known species tree and is highly efficient and accurate.
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TreeBeST is previously known as NJTREE. It has been largely used in the
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TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting
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group.
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This is the Ensembl Compara modifications version. The main new
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features are:
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1) -s option in treebest sdi, to allow a user-defined species tree.
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T node-tag in the NHX output: a bit-field listing the input trees
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2) that support the node.
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3) -I option in treebest nj, to carry on the T tags from the input tree
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4) -Z option in treebest best, to redefine the PhyML variable
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MIN_DIFF_LK
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5) -X option in treebest best, to give a higher weight to the
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likelihood that comes from the reconciliation with the species tree
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(default 1)
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6) -I option in treebest best, to start from the input tree instead of
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building one
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7) Species-intersection scores are now also reported as floating-point
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values under the DCS node-tag. The value is between 0 and 1, and
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displayed with 4 decimals.
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The script builds both the command line and GUI versions of treebest.
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