SlackBuilds Repository

14.2 > Academic > treebest-ensembl (1.9.2_git347fa82)

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.

This requires: fltk

Maintained by: Petar Petrov
Keywords: treebest,ensembl,phylogeny,tree,ML
ChangeLog: treebest-ensembl

Homepage:
https://github.com/Ensembl/treebest/

Source Downloads:
treebest-347fa82a0ce1c169849053fdc9ff7d19d221f290.tar.gz (619622cadea6da5d9c74defa761cfdda)

Download SlackBuild:
treebest-ensembl.tar.gz
treebest-ensembl.tar.gz.asc (FAQ)

(the SlackBuild does not include the source)

Validated for Slackware 14.2

See our HOWTO for instructions on how to use the contents of this repository.

Access to the repository is available via:
ftp git cgit http rsync

© 2006-2020 SlackBuilds.org Project. All rights reserved.
Slackware® is a registered trademark of Patrick Volkerding
Linux® is a registered trademark of Linus Torvalds
Web Design by WebSight Designs |  Managed Hosting by OnyxLight Communications