TreeBeST: Tree Building guided by Species Tree (Ensembl Compara modifications)
Pull request Compare This branch is 31 commits ahead of lh3:master.
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
align_lib Rely on the system getopt header Apr 9, 2017
common Fixed a GCC warning May 13, 2014
examples Moved from treesoft.sf.net SVN Feb 17, 2011
phyml Added an option to scale the log-likelihood of the species-tree-based… Jan 21, 2014
scripts Moved from treesoft.sf.net SVN Feb 17, 2011
ACKNOWLEDGEMENTS Moved from treesoft.sf.net SVN Feb 17, 2011
AUTHORS Moved from treesoft.sf.net SVN Feb 17, 2011
COPYING Moved from treesoft.sf.net SVN Feb 17, 2011
ChangeLog Moved from treesoft.sf.net SVN Feb 17, 2011
FUTURES Moved from treesoft.sf.net SVN Feb 17, 2011
INSTALL Moved from treesoft.sf.net SVN Feb 17, 2011
Makefile bugfix: Bison can crash if YYINITDEPTH is too small. Jan 24, 2017
Makefile.mac Moved from treesoft.sf.net SVN Feb 17, 2011
NEWS Moved from treesoft.sf.net SVN Feb 17, 2011
PROBLEMS Moved from treesoft.sf.net SVN Feb 17, 2011
README.md New per-release tags Jun 23, 2014
algo.h algo.h now uses standard libs (no "extern" ref.) Apr 9, 2017
align.c "double" instead of "float" and MIN_DIFF_LK command line option Oct 2, 2013
align.h "double" instead of "float" and MIN_DIFF_LK command line option Oct 2, 2013
aln_mask.c "double" instead of "float" and MIN_DIFF_LK command line option Oct 2, 2013
backtrans.cc "double" instead of "float" and MIN_DIFF_LK command line option Oct 2, 2013
best.c New parameter to return immediately after having created the filtered… Apr 9, 2017
best.h New parameter to return immediately after having created the filtered… Apr 9, 2017
brent.c Moved from treesoft.sf.net SVN Feb 17, 2011
bs_nj.c Fixed a few C warnings Jan 21, 2014
compare.cc added skip_mmerge support Feb 21, 2011
cpp_utils.cc Moved from treesoft.sf.net SVN Feb 17, 2011
cpp_utils.h Moved from treesoft.sf.net SVN Feb 17, 2011
cut_tree.c Moved from treesoft.sf.net SVN Feb 17, 2011
doxygen.conf Moved from treesoft.sf.net SVN Feb 17, 2011
eps.h "double" instead of "float" and MIN_DIFF_LK command line option Oct 2, 2013
est_len.c Moved from treesoft.sf.net SVN Feb 17, 2011
filter.c Moved from treesoft.sf.net SVN Feb 17, 2011
flcallback.cc Moved from treesoft.sf.net SVN Feb 17, 2011
flglobal.cc "double" instead of "float" and MIN_DIFF_LK command line option Oct 2, 2013
flglobal.h added information of support evidence for each node Feb 21, 2011
flnjtree.cc Moved from treesoft.sf.net SVN Feb 17, 2011
flnjtree_ui.fl Moved from treesoft.sf.net SVN Feb 17, 2011
flworkspace.cc "double" instead of "float" and MIN_DIFF_LK command line option Oct 2, 2013
lost.c Moved from treesoft.sf.net SVN Feb 17, 2011
main.c Moved from treesoft.sf.net SVN Feb 17, 2011
make_ng86.c "double" instead of "float" and MIN_DIFF_LK command line option Oct 2, 2013
make_ng86.h Moved from treesoft.sf.net SVN Feb 17, 2011
mmerge.cc Empty trees allowed Oct 2, 2013
ng86_ds.c Moved from treesoft.sf.net SVN Feb 17, 2011
nhx_output.cc The duplication confidence score is given with DCS May 13, 2014
nj.c Moved from treesoft.sf.net SVN Feb 17, 2011
nj2.c "double" instead of "float" and MIN_DIFF_LK command line option Oct 2, 2013
order.c "double" instead of "float" and MIN_DIFF_LK command line option Oct 2, 2013
ortho.c The duplication confidence score is given with DCS May 13, 2014
output.c Fixed a few C warnings Jan 21, 2014
parser.l Moved from treesoft.sf.net SVN Feb 17, 2011
parser.y "double" instead of "float" and MIN_DIFF_LK command line option Oct 2, 2013
phyml.c fixup lk_scale Apr 9, 2014
phyml.h Added an option to scale the log-likelihood of the species-tree-based… Jan 21, 2014
pre_cons.c Moved from treesoft.sf.net SVN Feb 17, 2011
prob_dist.c Moved from treesoft.sf.net SVN Feb 17, 2011
read.c Fixed a few C warnings Jan 21, 2014
read_aln.cc Moved from treesoft.sf.net SVN Feb 17, 2011
reroot.c "double" instead of "float" and MIN_DIFF_LK command line option Oct 2, 2013
sdi.c Treebest sdi doesn't like unary nodes May 4, 2018
simulate.c "double" instead of "float" and MIN_DIFF_LK command line option Oct 2, 2013
spec-ens.nh Moved from treesoft.sf.net SVN Feb 17, 2011
spec-enstax.nh Moved from treesoft.sf.net SVN Feb 17, 2011
spec-taxon_id.nh Moved from treesoft.sf.net SVN Feb 17, 2011
spec.c Moved from treesoft.sf.net SVN Feb 17, 2011
spec.nh Moved from treesoft.sf.net SVN Feb 17, 2011
subtree.c Moved from treesoft.sf.net SVN Feb 17, 2011
task.c Fixed tree_support output ("T" NHX tag) Oct 2, 2013
timeout.c Moved from treesoft.sf.net SVN Feb 17, 2011
tree.h SIS is now a double, and is printed with 2 decimals Apr 9, 2014
tree_plot.c "double" instead of "float" and MIN_DIFF_LK command line option Oct 2, 2013
tree_plot.h "double" instead of "float" and MIN_DIFF_LK command line option Oct 2, 2013
treebest.texi Moved from treesoft.sf.net SVN Feb 17, 2011
trimpoor.cc Moved from treesoft.sf.net SVN Feb 17, 2011
utils.h Moved from treesoft.sf.net SVN Feb 17, 2011
utils1.c Moved from treesoft.sf.net SVN Feb 17, 2011
utils2.c "double" instead of "float" and MIN_DIFF_LK command line option Oct 2, 2013

README.md

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