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NEWS
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Beta Release 1.9.2 (19 October, 2007)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
A year later, release 1.9.2 comes out, and from this release, NJTREE
will be formally renamed as `TreeBeST' which stands for `(gene) Tree
Building guided by Species Tree'. It is a long story about how this name
comes and I may not explain this here. Anyway, this project has a more
appropriate name.
Few improvements were made in the past one year. However,
TreeBeST/NJTREE was intensively used by both TreeFam and EmsemblCompara,
is proved to be highly accurate and robust in practice. As for the
changes in this new release, here is the list:
* Added `trimpoor' command, which recursively removes sequences that
lead to a lot of spurious duplications and losses.
* Added a Makefile for Mac OS X. Universal binary can be built.
* Fixed a typo in the species tree.
* Added quiet mode to `treebest best'.
(1.9.2: 19 October 2007, r278)
Beta Release 1.9.1 (25 October, 2006)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This is a bug fix release. Now njtree can be correctly packaged. We also
fixed a potential memory violation, although that never happened. A new
function to calculate an "SIS" (Species Intersection Score) was
added. This score is the percentage overlap between the two species sets
that are descendant from the two daughters of a duplication node. Higher
value indicate more reliablity.
We are sorry for the obvious bugs in the previous release, and hope you
enjoy the new one.
Beta Release 1.9.0 (10 October, 2006)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This is the last release managed by the CVS located on my own laptop. I
will migrate the whole NJTREE source codes to treesoft subversion
repository, hosted by SourceForge.net. The historical version before
this release of NJTREE cannot be tracked any longer, but ChangeLog is
still available showing the path of NJTREE.
From this release, NJTREE will be released more frequently. The version
number will also differ from the previous ones. I will not use "release
candidate" or "rc" any more. Instead, version is always named by "x.y.z"
where "x" indicates major version, "y" minor version and "z" means bug
fix release. A release can be a beta one, which will be clarified in the
corresponding release note, but is not always visible from the version
number.
So far as subversion structures are concerned, release and beta release
will always stay at the top of "trunk". A "dev" will be created in
"branches" for main-thread development. A tag will be applied to each
release or beta release. I prefer not to create a branch for bug fixes
unless this is absolutely necessary. Bug fixes usually happen at the top
of "dev" branch and then will be merged to the "trunk".
Now, come to the changes since release 1.0.0. The most notable changes
in this release is the use of a species tree and/or a constraining tree
in building ML trees. This is done by multiplying extra likelihood terms
to the original likelihood calculated from sequences evolution. During
the development of this function, I also made it possible to root a gene
tree by SDI in O(N^2) time (or O(N logN) in average). Fast rooting makes
the new tree builder practically useful. Other minor changes are:
* Infer apparent orthologs, named by Ensembl Compara group. But my
definition is slightly different from theirs.
* Accelerate several functions.
* Improve the command-line interfaces for `phyml' and `best' modules.
* Compatible with gcc-3.4 and gcc-4.1.
* Compatible with MINGW and MacOS X.
* Add more species into the species tree. Now in the mammalian group,
the topology of the species tree is identical to the NCBI
taxonomy. However, for now I do not know whether this is a good idea
or not.
Release 1.0.0 (06 July, 2006)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
After nearly two years, I decide to release the first version
1.0.0. This does not mean I plan to stop the project, but means I
prepare to inject new methods and ideas which may impair the stability
of the current codes. NJTREE-1.0.0 has been heavily tested in building
TreeFam-3, and is proved to be quite stable when TreeFam data are
provided.
Notable changes are:
* New modules: 'pwalign', 'mmerge', 'sortleaf' and 'estlen'.
* New distance: nt-mm, the mismatch distance for nucleotide alignment.
* Merge multiple trees. Functions for merging two trees are removed. The
new algorithm is also able to consider bootstrapping supports. Now
'dm' tree is built by merging 'dn', 'ds' and 'ntmm' trees, and 'best'
tree by merging the three trees above plus 'phyml-HKY' and 'phyml-WAG'
trees.
* PHYML part:
1. Accelerate PHYML by about 20%.
2. Integrate PHYML to FLNJTREE, the NJTREE GUI.
3. Add names of internal nodes to the PHYML tree.
4. PHYML bootstrapping is avaible.
* Mask low-scoring segments. See CLUSTALX paper for more description.
* Calculate topological distance (Robinson-Foulds distance) between two
trees.
* TreeFam-3 species tree.
* Reserve NHX information of the input tree.
* A lot of bug fixes.
Beta Release 0.2.0-rc5 (01 December, 2005)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
A lot of bug fixes and improvements have been achieved since the last
release. Integrating `align_lib' and hash library written by me, and
the masterpiece `phyml' as well, njtree becomes more powerful and
flexible. It is now capable of constructing ML tree, building
protein-guided nucleotide alignment, reordering leaves and many other
new functions. It also comes with a GUI which will make biologists feel
more friendly.
Notable changes are:
* Incorporate phyml. ML tree and likelihood mapping are available.
* Implement GUI (Graphical User Interface) by using FLTK, a
cross-platform GUI library.
* Build protein-guided nucleotide alignment.
* Reorder leaves according to another tree, or to the species of the leaves.
This will make it easy to compare similar trees.
* Information stored in NHX format is now fully parsed and stored in a
hash. Tag `Sd' and `G' will also be added by `njtree' itself instead
of by additional scripts.
* Implement unrooted constrained NJ for binary constraints.
* Simulate a gene tree based on a species tree by randomly generating
duplications and losses.
* A batch of bug fixes.
Version 1.0 will be released if no other bugs are found.
Beta Release 0.2.0-rc4 (10 April, 2005)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
It is a long time, and finally a new beta release is coming out. It
seems that I have forgotten to add a tag for 0.2.0-rc3, and so I can
only compare the current version with tag RELEASE-0-2-0-rc2-bk9 that is
presumably identical to 0.2.0-rc3.
The most notable change in this release is "tree merging" strategy. By
tree merging, dS and dN trees can be combined in a more reasonable way.
Other changes include:
* Implement a new algorithm to do gene loss inference. This one complies
with the original meaning of `gene loss'.
* Add Du Wenfeng to AUTHOR.
* Add `distmat' component.
* Add time limit to tune the number of bootstraps.
* Code clean-up, efficiency improvements and numerous bug fixes.
Beta Release 0.2.0-rc3 (28 January, 2004)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
We here claim a new beta release of NJTREE. Bugs are fixed and many new
functions added including SDI tree rooting, improved ortholog inference,
dN-dS mixed distance, and leaf, mfa2aln and ortho components.
Other notable changes are:
* `leaf' component: get names of external nodes `mfa2aln' component:
convert fasta format to quality-assigned aln format `ortho' component:
ortholog inference
* Add version checking in run_njtree.pl and cgi_njtree.pl.
* Remove gapped columns in multialignment
* Output full FASTA header line
Many new functions are added to BRANCH-0-2-0-rc2-bk9, an unstable
working branch for the next release.
Beta Release 0.2.0-rc2 (12 December, 2004)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The major revisions in this release include adding nucleotide alignment
support and NJTREE user's manual. Now phylogenetic trees can be built
from nucleotide alignment in coding regions with d_s or d_n distances.
Other notable changes are:
* Fix SDI bugs when multifurcated species nodes are encountered. In
previous release, this function is not fully tested.
* Fix floating point exception on alpha-True64.
* Add `trans' and `filter' components.
* nh2pic can still be compiled when GD package is lacked, but only EPS
output is support at this time.
Beta Release 0.2.0-rc1 (29 November, 2004)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This is the first formal release of njtree, a tree-builder by
constrained neighbour-joining algorithm. This package is also capable of
SDI (Speciation vs. Duplication Inference), tree rooting, figure output
and many other utilities, facilitating tree-building routains.
Njtree is initiated by TreeFam project inspired by Richard Durbin. The
basic idea is to build a full tree constrained by the human curated seed
tree. As we will handle a batch of large trees, this process must be
controlled and fast enough. Allowing for multifurcated nodes makes the
things more complex: SDI algorithm only works with binary species
trees. These demands disqualify all the current softwares. So we wrote
njtree, a fast and capable tree builder according to these
requirments. The basic framework of njtree might not be brand-new, but
njtree must be the program you want in practice.