Add LICENSE
Remove unneeded MESSAGE file
Upstream changes:
Version 2.1
----------------------------------------------------------------------
* Fixed bug 196 "clustalx: user feedback about use of secondary structure
printed to console" - secondary structure is now used if specified
in Alignment -> Alignment Parameters -> Secondary Structure Parameters
UserParameters->getGui() should be used when ClustalW code needs to
know if a function has been called from ClustalX
* Fixed bug 204 "Nexus alignment format contain invalid line" - the amino
acid alphabet line has been removed
* Missing/corrupted file names in ClustalX status messages have been
fixed
* Fixed bug 175 "msf/pileup files cannot be read if sequences names are
all numbers" - this happened if a line such as
528244 .......... .......... .......... .......... ..........
was present in the first block of the file
* Fixed bug 192 "Alignment in Phylip Format broken for big Alignments"
* Fixed bug 198 "Warning about divergent sequences gets printed to
console in ClustalX"
* Fixed bug 151 "clustalx doesn't switch to profile alignment mode when
profile12 is given on cmdline"
----------------------------------------------------------------------
Version 2.0.12
----------------------------------------------------------------------
* Fixed bug 189 "Fixed filename used for iteration":
Now Creating temporary file and added error check
* Fixed bug 180 "Pairwise NJ tree: final bracket missing"
* Fixed bug 178 "Seg-fault on 64bit when -quicktree -upgma for sequences with high identity":
Using relative error now to avoid unsafe comparison which led to
incorrect branching
* Fixed Bug 176 "iteration doesn't iterate if -usetree is used as well"
* Fixed bug 162 "percent identity file option in clustalW not working":
Added -pim as command line option. See help
* Fixed bug 155 "upgma trees cannot be read"
* Fixed bug 147 "report duplicate sequences":
"ClustalW/X now report offending sequences which are empty, duplicates etc
* Fixed bug 134 "Exit when encountering unrecognized cmdline params":
ClustalW now exits when encountering invalid values for command line
arguments instead of just reverting to default values
* Fixed bug 185 "clustal alignments differ between interactive and commandline mode"
window-gap and ktuple initialisation now fixed and made the same
between commandline and interactive mode
* Fixed bug 184 "error messages are send to stdout"
* Fixed bug when weights are 0, and nseq > INT_SCALE_FACTOR in UPGMA
code (see RootedGuideTree.cpp)
* General code cleanup
- Introduced return values where control reached end of non-void function
- Removed unused variables
- Removed comparison between signed and unsigned integer expressions
- Removed deprecated conversion from string constant to char*
----------------------------------------------------------------------
Version 2.0.11
----------------------------------------------------------------------
* fixed file extension bug 166 in interactive mode
* Fixed bug 169, memory violation for DNA/RNA k-tuple
* Cut down distance calculation, symmetric matrix
----------------------------------------------------------------------
Version 2.0.10
----------------------------------------------------------------------
* Fixed g++-4.3 compilation errors
* Added new -quiet command line flag
* Added new -stats=<file> command line flag
* Fixed bug 142: command separator can now be mixed "/" and "-" on all platforms
* Fixed bug 141: profile merging and saving failed
* Fixed bug 139: saving of column quality scores
* Updated help files (new flags, new colour parameter format)
----------------------------------------------------------------------
Version 2.0.9
----------------------------------------------------------------------
* GUI now responding and giving feedback during alignment
* automatic automake os detection
* new OS_ define (set by clustalw/configure clustalx/clustalx.pro)
* got rid of qt3 dependencies
* removed QScrollArea bug workaround (fixed in Qt 4.3)
* Fixed bug 135: Last sequence and last residue not displayed on MacOSX
* Fixed bug 123: secondary structure profile alignment in clustalX on Mac
* Fixed g++-4.3 build error (include climits.h)
----------------------------------------------------------------------
Version 2.0.8
----------------------------------------------------------------------
* Implemented maxseqlen cmdline switch
* Updated help-file
* Fixed Bug 123: loading profile using gap penalties (ClustalX, Mac)
* Fixed bug 133: providing profiles on command line fails (ClustalX)
* Fixed bug 125: Angle bracket inside sequence
* Fixed bug 129: Early exit on empty sequence
* Fixed a couple of possible memory leaks
----------------------------------------------------------------------
Version 2.0.7
----------------------------------------------------------------------
* Fixed bug 121: CRLF in sequence names (Pearson) are not trimmed
* Fixed bug 122: convert option broken
* Fixed reopened bug 114: profile alignment input didn't work with new
getSeqRange routines
* Fixed bug 119: build with g++ 4.3
----------------------------------------------------------------------
Version 2.0.6
----------------------------------------------------------------------
* Fixed bug 77: fasta input performance issue
* Fixed bug 114: segfault while doing profile alignment with secondary
structure mask
* Removed unncessary id console output in EMBLFileParser.cpp
* Fixed Bugs 108 and 109 and allowed mixed-case command line options
----------------------------------------------------------------------
Version 2.0.5
----------------------------------------------------------------------
* Fixed bug 105: Disallowed combination of "Reset Gaps"
and Iteration in GUI
* Fixed bug 104 "reset all gaps doesn't work"
* Changed command line separator for Mac to hyphen instead slash
* Fixed full command line parsing for ClustalX after help flag
----------------------------------------------------------------------
Version 2.0.4
----------------------------------------------------------------------
* Updated URLs in help files
* Fixed bug 96: error message when loading alignment with identical
sequence names
* Made console output look more like 1.83
* Fixed bug 100: "Scores in clustalw2.0 don't match clustalw1.83"
getMatrix was called with wrong scaling factor
* Fixed bug 99: "stars in input not ignored"
Asterisks were changed to gaps in alignment
* New command line option: -fullhelp which dumps the built-in help
file content.
* Quickfix for bug 94 "quicktree seqfault"
----------------------------------------------------------------------
<= Version 2.0.3
----------------------------------------------------------------------
* Added LICENSE file to distribution
This file contains the information about commercial licensing of
clustal as well as FAQ for licensing issues
* Added README file to distribution
This is the file that lists the files and directories on the Clustal
FTP site. It also includes acknowledgements of people who have
contributed binaries
* Removed .pro Qt file from the distribution
pro-file should be generated anew using qmake and modified according
to build requirements, i.e. no need for version control.
* Fixed bug where ClustalX2 was not processing command line args
* Fixed Segfault on opening helpfile. Happened on Linux only with -O2
and when calling binary directly, not using the wrapper
* Added debian packaging files
* Added support for help command line flag GUI/xmenus version
When requesting help file, graphical version of command line help is
displayed (1.83 tried to open clustalw help)
* Added complete automake (configure etc) system according to the
following websites:
- http://www.openismus.com/documents/linux/automake/automake.shtml
- http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
* clustalw files source files have been moved to subdir
* Fixed bug #53 change MAXNAMESTODISPLAY back to 10 from 30.
This fixes problem of large amount of space between sequence name and
actual alignment in clustal output files
* This solves bug #72 with long lines (5000+) in fasta files
changed code to use strings rather than arrays. Needed to add delim
parameter to getline in order to read files formatted for different
OSs on different platforms.
* Fixed Bug 79:
"The count of amino acids in the ClustalX Postscript output not correct"
Off-by-one issue
* ClustalX and ClustalW version numbers are now the same and defined in
ClustalW code (automake)
* Fixed problem with compilation of ClustalX2 with gcc3
avoiding gcc3 error message: cannot declare member function
QDir::currentPath'
* Target now clustalw2 instead of clustalw
* Fixed Bug 46
added in aminoacid code O for pyrrolysine
* Fixed bug 89
changed clustalw2.0 to conform to 1.83 behaviour for width of sequence
ID and alignment
* Fixed bug 90
changed clustalw2.0 to conform to 1.83 behaviour leading spaces are
stripped from FASTA identifiers.
* Fixed bug 91
Clustalw2.0 now handles pseudo-FASTA/MoST format files. Strips out
numbers and spaces.
Packaged by Jason Bacon for pkgsrc-wip.
PLINK/SEQ is an open-source C/C++ library for working with human genetic
variation data. The specific focus is to provide a platform for analytic tool
development for variation data from large-scale resequencing and genotyping
projects, particularly whole-exome and whole-genome studies. It is independent
of (but designed to be complementary to) the existing PLINK package.
libXext/buildlink3.mk, now that it is included there.
Leave the places where its API version is set or variables from it
are used directly (about 3 packages).
From Jason Bacon via pkgsrc-wip.
PLINK is a free, open-source whole genome association analysis
toolset, designed to perform a range of basic, large-scale
analyses in a computationally efficient manner.
The focus of PLINK is purely on analysis of genotype/phenotype
data, so there is no support for steps prior to this (e.g. study
design and planning, generating genotype or CNV calls from raw
data). Through integration with gPLINK and Haploview, there is
some support for the subsequent visualization, annotation and
storage of results.
Changelog:
Version 0.12.13
GChemPaint:
* Fix View::BuildSVG() and View::BuildEPS() which were missing the
trailing 0.
* Fix loading of arrows inside a group. [#27032]
Remove devel/py-ctypes (only needed by and supporting python24).
Remove PYTHON_VERSIONS_ACCEPTED and PYTHON_VERSIONS_INCOMPATIBLE
lines that just mirror defaults now.
Miscellaneous cleanup while editing all these files.
Notable changes in Gromacs 4.5.5:
* Improved pdb2gmx -chainsep option and reintroduced the -merge option.
* Fixed mdrun file appending truncating files to 0 bytes when
continuation runs stopped before writing new output.
* Fixed COM pulling with multiple constraints checking the
convergence of one constraint instead of all.
* Fixed some dihedrals in sugars in Gromos53a5/6 working on the wrong atoms.
* AmberGS force field is now based on Amber94 instead of Amber96.
* Moved hydrogens in Charmm27 protein termini to separate
charge groups and added ACE and CT3 residue types.
* Many small fixes which avoid termination with fatal errors
or crashes in mdrun and tools.
* Many small updates to the manual pages of programs.
Changelog:
Fixes and enhancements in chemtool 1.6.13
- New export option "ASY" for Asymptote files (http://asymptote.sourceforge.net)
- Added support for Unicode symbol characters inserted e.g. by cut-and-paste from LibreOffice
- Fixed build with newer linkers that do not resolve indirect requirements automatically
- Rewritten logic for choosing to include national language support during build
- Fixed crash on startup due to errors in menu icon setup
- Batch mode could crash due to incomplete initialisation of color arrays
- Undo/redo in "move fragment"-mode did not work as intended
- Default extension is now appended to the save filename as needed
- Fixed exporting to files or directories containing spaces in their names
Changelog:
Version 0.12.10
GCrystal:
* show only atoms from the first crystal when loading a CIF file
with several structures.
* don't crash when loading a file with invalid atoms.
* don't display two atoms at the same position.
* don't loose the radius ratio on serialization.
Other:
* fix build with most recent glib-2.0 and xulrunner.
* enhanced translation: de.
Primer3 is a widely used program for designing PCR primers (PCR =
"Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool
in genetics and molecular biology. Primer3 can also design
hybridization probes and sequencing primers.
GChemPaint, a 2D chemical editor and some other programs related to chemistry
suitable for the GNOME desktop.
The Gnome Chemistry Utils include three utilities:
- a 2D chemical editor (GChemPaint).
- a chemical calculator (computes raw formule, molar weight, mass composition,
etc..) and isotopic pattern).
- a molecule 3d viewer using OpenGL to display molecular models.
- a crystal structues viewer and editor.
- a periodic table of the elements.
- a spectrum viewer.
These programs are based on an included C++ library which provides a few
widgets and various classes, some related to chemistry and some utility
classes.
Open Babel is a chemical toolbox designed to speak the many languages
of chemical data. It's an open, collaborative project allowing
anyone to search, convert, analyze, or store data from molecular
modeling, chemistry, solid-state materials, biochemistry, or related
areas.
