(ChangeLog)
2012-08-20 Paolo Tosco <paolo.tosco@unito.it>
* src/formats/mol2format.cpp: added a check for N.4 nitrogens
(fixes PR#3557898)
2012-06-09 Paolo Tosco <paolo.tosco@unito.it>
* src/kekulize.cpp: reverted the r4862 patch to kekulize.cpp;
the incorrect aromaticity perception of oxonium salts concerned
only the MOL2 format, so the fix was applied to mol2format.cpp
instead
* src/formats/mol2format.cpp: added a check to improve downstream
aromaticity perception on charged molecules containing oxygen
2012-06-07 Paolo Tosco <paolo.tosco@unito.it>
* include/openbabel/atom.h: added protos for CountFreeSulfurs() and
IsThiocarboxylSulfur() functions which are equivalent to
CountFreeOxygens() and IsCarboxylOxygen() and address
(di)thiocarboxyl groups
* src/atom.cpp: added the CountFreeSulfurs() and
IsThiocarboxylSulfur() functions
* src/forcefields/forcefieldmmff94.cpp: added some additional
checks to make MMFF94 atom type assignment more robust
* src/formats/mol2format.cpp: added some checks to improve downstream
aromaticity perception on charged molecules containing nitrogen,
oxygen and sulfur
* src/kekulize.cpp: added a check to fix incorrect perception of
aromatic oxonium and thionium cations
(NEWS)
Open Babel 2.3.1 (2011-10-14)
This release represents a major bug-fix release and is a stable
upgrade, strongly recommended for all users of Open Babel. Many bugs
and enhancements have been added since the 2.3.0 release.
Citation:
Please consider citing this work if you publish work which used Open Babel:
Noel M. O'Boyle , Michael Banck , Craig A. James , Chris Morley , Tim
Vandermeersch and Geoffrey R. Hutchison. "Open Babel: An open
chemical toolbox." Journal of Cheminformatics 2011, 3:33.
http://dx.doi.org/10.1186/1758-2946-3-33
Upstream changes:
1.6.924
[Significant changes]
* Bug/feature issue tracking has moved to GitHub Issues:
https://github.com/bioperl/bioperl-live/issues
* DB_File has been demoted from "required" to "recommended",
which should make easier for Windows users to install BioPerl
if they don't need that module.
[New features]
* Bio::Search::HSP::GenericHSP
- Bug #3370, added a "posterior_string" method to retrieve the
posterior probability lines (PP) from HMMER3 reports [fjossandon]
- Added a "consensus_string" method to retrieve the consensus
structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
* Bio::SearchIO::hmmer2
- The number of identical and conserved residues are now calculated
directly from the homology line [fjossandon]
- Now the Query Length and Hit Length are reported when the alignment
runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
- Implemented the capture of the consensus structure lines [fjossandon]
* Bio::SearchIO::hmmer3
- The number of identical and conserved residues are now calculated
directly from the homology line [fjossandon]
- Now the Hit Length is reported when the alignment runs until the end
of the sequence/model ('.]' or '[]') [fjossandon]
- Implemented the capture of the consensus structure lines [fjossandon]
- Implemented the capture of the posterior probability lines [fjossandon]
- Completed the development of NHMMER parsing, including alignments [fjossandon]
* Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
- Feature #2615, moved "_init_parse_params", "max_significance, "signif",
"min_score", "min_bits, and "hit_filter" methods from
'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
This means that the Bio::SearchIO->new() parameters '-signif', '-score',
'-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
besides Blast, instead of being ignored. Added tests for all moved methods
using HMMER outputs and run the full test suite and everything pass [fjossandon]
* Bio::SeqIO::MultiFile
- Autodetection of file format [fangly]
* Bio::Tools::GuessSeqFormat:
- Format detection from non-seekable filehandles such as STDIN [fangly]
[Bug fixes]
* Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
* Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
* SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
* Abstract: Fixed ActivePerl incapability of removing temporary files
because of problems closing tied filehandles [fjossandon]
* IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
because ActivePerl were producing a ".index.pag" and ".index.dir"
files instead of a single ".index" file (like Strawberry Perl).
Now those temporary files are correctly considered and deleted. [fjossandon]
* Test files: Added missing module requirements (DB_File and Data::Stag)
to several tests files that were failing because those modules were
not present. Now those test files are correctly skipped instead. [fjossandon]
* Blast: Added support to changes in bl2seq from BLAST+ output, which
now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
* Phylip: Return undef in "next_aln" at file end to avoid
an infinite loop [yschensandiego]
* HMMER3: When a hit description is too long, it is truncated in
the Scores table. In those cases, the more complete description from
the Annotation line (>>) will be used [fjossandon]
* GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
since it is now used by HMMER3 format in alignments [fjossandon]
* GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
to return undef if the query/hit length is unknown (like in some
HMMER outputs), to avoid division by 0 crashes. Also "query_length"
now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
* HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
added support to multi-query reports, reduced code redundancy,
and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
* [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
* [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
* [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
* Fixed some Bio::Root::Utilities subroutines [fjossandon]
* Double-quotes on paths are needed in some places [fjossandon]
* [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
* Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
* Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
with the latest changes made in their own repositories [fjossandon]
* General synching of files with the master branch [fjossandon]
* Fixed tests failing in Windows because of using Linux commands [fjossandon]
* Closed many open filehandles that prevented temporary files deletion [fjossandon]
* Fixed broken MeSH parser [fjossandon]
* Fixed missing detection of format in SeqIO when given a -string [fangly]
Do it for all packages that
* mention perl, or
* have a directory name starting with p5-*, or
* depend on a package starting with p5-
like last time, for 5.18, where this didn't lead to complaints.
Let me know if you have any this time.
Bio::ASN1::EntrezGene is a regular expression-based Perl Parser for NCBI Entrez
Gene genome databases (http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene). It
parses an ASN.1-formatted Entrez Gene record and returns a data structure that
contains all data items from the gene record.
Fixes and enhancements in chemtool 1.6.14
- Updated configure script to support ARM64.
- Fixed potential crash during EPS output.
- Fixed detection of openbabel 2.3.x
to address issues with NetBSD-6(and earlier)'s fontconfig not being
new enough for pango.
While doing that, also bump freetype2 dependency to current pkgsrc
version.
Suggested by tron in PR 47882
a) refer 'perl' in their Makefile, or
b) have a directory name of p5-*, or
c) have any dependency on any p5-* package
Like last time, where this caused no complaints.
File too long (should be no more than 24 lines).
Line too long (should be no more than 80 characters).
Trailing empty lines.
Trailing white-space.
Trucated the long files as best as possible while preserving the most info
contained in them.
MPQC is the Massively Parallel Quantum Chemistry Program.
It computes properties of atoms and molecules from first
principles using the time independent Schroedinger equation.
It runs on a wide range of architectures ranging from single
many-core computers to massively parallel computers. Its design
is object oriented, using the C++ programming language.
Capabilities
* Closed shell, unrestricted and general restricted open shell
Hartree-Fock energies and gradients
* Closed shell, unrestricted and general restricted open shell
density functional theory energies and gradients
* Second order open shell perturbation theory (OPT2[2]) and
Z-averaged perturbation theory (ZAPT2) energies.
* Second order closed shell Moller-Plesset perturbation
theory energies and gradients.
* Second order Moller-Plesset perturbation theory
including an R12/F12 correlation factor. Energies of closed-
and open-shell systems are supported.
* Explicitly-correlated R12/F12 coupled-cluster methods via
interface to Psi3 code and via native (experimental)
implementation.
* Explicitly-correlated multireference methods (MRCI, CASPT2)
via interfaces to GAMESS and MOLCAS codes.
* Robust internal coordinate geometry optimizer that efficiently
optimizes molecules with many degrees of freedom. Nearly
arbitrary internal coordinate constraints can be handled.
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.
from wip/chemical-mime-data
The chemical-mime-data package is a collection of data files to add support
for various chemical MIME types on Linux/UNIX desktops, such as KDE and GNOME.
Chemical MIMEs were proposed in 1995, though it seems they have never been
registered with IANA. But they are widely used and the project's aim is, to
support these important, but unofficial MIME types.
The Blue Obelisk Data Repository lists many important chemoinformatics
data such as element and isotope properties, atomic radii, etc.
including references to original literature. Developers can use
this repository to make their software interoperable.
* Fixed pdb2gmx picking up force field from local instead of
library directory
* Made pdb2gmx vsite generation work again for certain His namings.
* Fixed incorrect virial and pressure averages with certain
nst... values (instantaneous values correct)
* Fixed incorrect cosine viscosity output
* New -multidir alternative for mdrun -multi option
* Several minor fixes in analysis tools
* Several updates to the program documentation
This is maintainance release, it fixes:
* Double precision energy file reading
* CHARMM and GB issues
* Support for Altivec (PowerPC) with CMake
* Running binaries within the CMake build tree is now possible
* Various other issues
Based on PR#43775 by Kamel Derouiche.
5.2 14.07.2004 - Version 5.2 !!!
NEW RELEASE
===========
5.2.rc17 14.07.2004 - Manual sources moved out of the package
- numerous changes in the manual
5.2.rc16 12.07.2004 - Makefile.am: double distclean rule removed
- fflush added before mygets() - because of Windows
- manual spell-checked
- '-consmrel' fixed
- usage message extended
5.2.rc15 09.07.2004 - many changes to the manual
5.2.rc14 01.07.2004 - test suite checked, notice about results added
5.2.rc13 01.07.2004 - a number of small fixes (alloc and dealloc in epe)
- convergence output for user branches fixed
- G-T rate output precision fixed
- tests checked and fixed
5.2.rc12 30.06.2004 - branch length convergence output corrected for
user set branch lengths (i.e. no estimate)
- avergedist updated: output of min/max/var/std.dev.
- tstvratio and yrtsratio - no output for GTR
- some future cmdline flags added to help
- -prefix, -sub50, -randseed moved to usage output
- -randseed=# added
- release date changed in code
5.2.rc11 18.06.2004 - flags to set epsilon values added for debugging
(dependent on USE_ADJUSTABLE_EPS compiler switch)
19.06.2004 - quartet percent computation fixed:
quartet sums moved qinfomatr[0] -> qinfomatr[8]
qinfomatr[0]=missing qs. (release 5.2.rc9)
- character state output added to R/Q matrix output
- average computation of dist-matrix changed:
mean=average, variance, std deviation
TODO: proper output / use Korbis S.E. method
25.06.2004 - GTR model ready, menu order HKY, TN, GTR, (SH), HKY
29.06.2004 - many changes to the manual
5.2.rc10 11.06.2004 - fixed no quartets in parameter estimtion for <4 seqs
15.06.2004 - computation of Bayesian weights moved into
subroutine loglkl2weight.
- use subroutine loglkl2weight in parallel code
-> fixing division by zero bug
5.2.rc9 11.06.2004 - sequence number check for <4 and >257 added
<4 - no quartet methods available
>257 - no quartet puzzling available
- counting for missing quartets added for parallel
message checking (TODO: handling and checking)
- output of root branch name added for clock analysis
(sequence name or "internal branch")
5.2.rc8 04.05.2004 - tree tests move to treetest.c/treetest.h
- comments added
- typo corrected (suset -> subset)
08.06.2004 - ELW: continue counting p, when significantly worse
- 1sKH/2sKH: restrict tests to 3 digits (0.00)
(test behaviour: seems not to use some trees (KH),
see above - used, but too low variance)
5.2.rc7 12.02.2004 - corrected typos in usage/README
20.02.2004 - cmdline: prefix flag fixed
22.02.2004 - '-wsr/-wsl' flags fixed: output file
and file name output
5.2.rc6 25.11.2003 - 'FPRINTF...' changed to 'fprintf(STDOUT,'
- strcpy added in openfile-routines
5.2.rc5 25.11.2003 - filename length chack added
- typo FILENAMELENTH corrected
5.2.rc4 19.11.2003 - minor corrections: int/uli comparisons
- SPRNG added to src/sprng
- src/sprng autoconf/automake setup
- Parallel Parameter Estimation (JPDC, Ekki 1)
5.2.rc3 07.11.2003 - WAG Matrix code/docu corrected (Goldman)
TODO: remove additional output for printrmat
TODO: make PEPS* smaller to have better accuracy
in parameter estimation.
5.2.rc2 01.09.2003 - bug from 5.1.pl29 found and eliminated
alloc size wrong: worked if Maxsubset<=Maxspc
TODO: remove out-commented debug messages
5.2.rc1 20.08.2003 - first release candidate for tree-puzzle 5.2
CODE FREEZE
===========
5.1.pl30 20.08.2003 - naming convention changed for manual name input to
use FILENAME.puzzle, ...
5.1.pl29 23.07.2003 - new compiler warnings fixed
- index error naming fixed
- debugging of matrix based permutation (not finished)
5.1.pl28 01.07.2003 - cmdline flags to switch off ml branch lengths
(-notreelh), tree tests (-notreetest)
5.1.pl27 24.06.2003 - output quartet support for incorporated split in
report file
5.1.pl26 06.06.2003 - menu order of tree reconstruction methods altered to
QP, user tree, consensus, dist (no tree)
(last two switched)
5.1.pl25 05.06.2003 - small changes to fix compiler warnings
5.1.pl24 04.06.2003 - changes from benchmark-branch merged:
debug output removed
- checktime fixed: sumtodo <-> done for quartets
5.1.pl23 26.05.2003 - puzzle.c: CONSENSUS -> QUARTPUZ,
allocated unnecessary memory
- additional malloc-checks added (if buffer == NULL)
01.06.2003 - mlmode conditions with readable constants (ml2.c,ml.h)
- garbage collection in tree2bipart/subtree2bipart
5.1.pl22 16.05.2003 - fixing Array Bound Read in fputid
(bug had no effect, but was read before check)
- garbage collection completed in p-step algorithms
and node-label (free_tree/internalnode),
trueIDtmp (allpstep),
- small fix in test script and rebuild of check-files
5.1.pl21 14.05.2003 - fixing free of all allocations in puzzling step
(mrca, recur, split, orig)
5.1.pl20 05.05.2003 - small fix in recursive Alg. (recur.c)
- debug output removed
- cross check removed from (recur.c,mrca.c)
5.1.pl19 27.04.2003 - recursive Alg. (recur.c) fixed:
edge cluster has not to be reconstructed after
adding new leaves only updated.
- debug output removed from recur.c, split.c
- MRCA-based (mrca.c) finished
5.1.pl18 26.04.2003 - recursive (recur.c) finished
TODO: remove debug output
- MRCA (mrca.c) startet
5.1.pl17 25.04.2003 - split-based (split.c) finished
TODO: remove debug output
- recursive (recur.c) startet
5.1.pl16 22.04.2003 - orig pstep alg: updating of edgemap outsourced to
updateedgemap_orig
- writeOTU_orig, writetree_orig, resetedgeinfo_orig,
minimumedgeinfo_orig:
_orig removed, since independent of algorithm type
- onepstep: _orig added (onepstep_orig)
- time check/status output moved to checktime routine.
added to ml step of parallel version
- split.c temporarily added to release
5.1.pl15 18.04.2003 - trueID dependent procedures 'de-trueID-ed'
trueID saved in the tips of the tree.
5.1.pl14 10.04.2003 - consensus stuff moved to consensus.h/.c
- unique tree sorting moved to treesort.h/.c
- changes to pstep-split.h/.c
- changed names of procedures using trueID to
*_trueID
5.1.pl13 07.04.2003 - subsetmatr.[hc] added to process missing data
analyses. (old version, functions in puzzle2)
- deglobalized: guessdatatype, readsequencefile,
getsizesites, initid, getseqs
removed obsolete: getdataset
- moved: output of taxa after input
- computation of Maxbrnch moved from readsequencefile
to inputandinit
- readsubsetfile, permutetaxa_ss added, '-rssm' works
- empty quartets fixed in checkquartet
missing data -> OK, HALT error otherwise
5.1.pl12 04.04.2003 - tests: check-qp-clock regenerated, changes in
Makefile.am and template-test
- obsolete stuff removed: global trueID_orig + alloc,
inittree_orig/freetree_orig from PP_SendDoPermutBlock
PP_slave_do_puzzling (ppuzzle), global _orig
variables (pstep), makenewsplitentries (old),
kh_test (old)
- column variable in tree output routines deglobalized
- copyright headers added to pstep.[hc]
- pstep copied to pstep-{split | mrca | recursive}
- implementation of pstep-split.[ch] started
(done: structure/init, todo: remove _orig stuff)
5.1.pl11 03.04.2003 - tests/Makefile.am: 'build-puzzle failed' fixed
- some changes in test script template
- cleanup: removed obsolete routines
- puzzle module: makenewsplitentriesnew
- ppuzzle module: PP_do_puzzling, PP_SendPermut,
PP_RecvPermut, PP_SendSplits, PP_RecvSplits
- deglobalized: makenewsplitentries, makepart,
computebiparts, copysplit
- parallel puzzling step based on allpstep, onepstep
- time check/status output added to parallel version
(inaccurate since current slave progress not known)
- TIMECHECK_INTERVAL for setting time interval
of status output in ML/puzzling step
- Header when printing 1 PAM rate matrix (-printrmat)
- final pstep copied to pstep-{split | mrca | recursive}
5.1.pl10 02.04.2003 - tests/Makefile.am fixed (TODO: build-puzzle.test)
- Dates/Version adjusted: April 2003/TREE-PUZZLE 5.2
- Dates/Version fixed in doc/*.html, doc/*.tex
- number added to outgroup(menu)/sequence(start) output
- Time measurement only done after each completed
intermediate tree to reduce the the number from
O(Numtrial*n^4) to O(Numtrial) -> less overhead,
but 15min met less accurate.
- quartet support output for splits added in
writeoutputfile for later use (TODO: '#if0'ed)
- (sequential) puzzling step moved from puzzle1.c
to pstep.c: allpstep, onepstep
TODO: parallel puzzling step in ppuzzle.c
(works but with old PP_slave_do_puzzling)
5.1.pl9 31.03.2003 - consensus construction added to menu
- support value computation fixed for phylip tree,
wrong divisor used in consensus
- test directory/Makefile.am/tests created
(make check)
5.1.pl8 30.03.2003 - puzzling step proc's: most variables 'deglobalized'
5.1.pl7 26.03.2003 - original puzzling step out-sourced to pstep-orig.c
and pstep-orig.h
pstep.c, pstep.h (and above) added to Makefile.am
5.1.pl6 25.03.2003 - '-usebranch' option added fr later use
- 'SONJA' added for external parameter estimation
5.1.pl5 24.03.2003 - ml branch length estimation added to consensus option
(todo: plausibility check - is tree file available)
- output for reportfile fixed
- output of likelihood to clocklike tree in treefile
added/fixed
5.1.pl4 21.03.2003 - consensus option added to compute usertree consensus
(only consensus is computed and printed to stdin)
- usertreefile PREFIX fixed
5.1.pl3 20.03.2003 - TP_MAX_EXP_DIFF=b-a>0 introduced, such that
(1.0+exp(a-b) == 1.0) to avoid the computation
as well as possible FPE, when a-b gets very small.
- flag '-prefix=XXX' added: use 'XXX' as filename
prefix instead of 'Infilename'
5.1.pl2 05.12.2002 - PP_Finalized before exit in parallel programs.
5.1.pl1 05.12.2002 - FPE in Brent's algorithm fixed: ()/0, when x=w=v.
5.1 05.11.2002 - Version 5.1 !!!
Based on PR#43776 by Kamel Derouiche for 15.7.
What's new in nut 15.8:
* This release updates the USDA database to include some data corrections for
milk.
* The program's initial data load is now considerably faster.
What's new in nut 15.7:
* This version includes an improvement to the automatic calorie tool to make it
better able to hold fat mass or lean mass constant.
* Also, there is now a facility to explicitly set the ratio between linoleic
and alpha-linolenic acids.
What's new in nut 15.0:
* This release introduces the new USDA Nutrient Database SR22 and allows
current nut installations to have their existing meal records reinterpreted
with the new database.
What's new in nut 14.5a:
* The new feature "Weight Log Regression" does not tell you what you weigh;
what it does is apply linear regression to a series of daily weight and body
fat percentage entries to smooth out the random noise and tell you which
direction your weight is trending, how fast it is going there, and how much
of the change is lean or fat.
Based on PR#43777 by Kamel Derouiche, with some clean up by me.
Version 1.20, 9/3/2008. This version fixes a bug that caused lucy
to fail when there was too much information on the FASTA header lines
in the input files. Lucy had a 256 character buffer for reading
lines from the input files. If any FASTA header lines were longer
than 256 characters, the remaining characters would get read as part
of the FASTA sequence. The solution implemented in this version is
simply to increase the buffer size to 4096 characters. While that
still leaves the potential for the same error to occur with extremely
long header lines, the limitation that this entails seems reasonable,
and this should fix the problem for all pratical purposes.
---------------------------------------------------------------------
Version 1.19, 12/30/2003. This version fixes a bug that could cause
sequences to be rejected incorrectly in the vector detection step
(phase 6). Because of the way that lucy compares "tags" in the
target sequence with "tags" in the vector sequence, some bases in
the target sequence could get counted more than once in the tally
of bases that match the vector sequence. In rare instances, this
could cause the sequence to exceed the minimum threshold for
rejection, as a result of random sequence similarity.
The reporting of the CLB range in the -debug output file has also
been changed. If the CLB range begins with the first base of the
sequence, then the left coordinate of the CLB range will be reported
as 1 (instead of 0). The range "CLB 0 0" still indicates an empty
CLB range.
GROMACS 4.5.1 is bug fix release.
Release notes for 4.5
New features
* Pencil decomposition of the reciprocal space PME grid to
improve scaling. This reduces the amount of communication
for high parallelization and improves load balancing with up
to 40% overall performance improvement for large systems.
* Memory usage is improved for very large systems, allowing
simulations of >100 million atoms.
* Running on a multi-core node now uses thread-based
parallelization to automatically spawn the optimum number of
threads in the default build. MPI is now only required for
parallelization over the network.
* Domain decomposition can now also be used without periodic
boundary conditions
* GPU acceleration support on NVIDIA cards. This first release
with GPU support based on OpenMM provides up to an order of
magnitude faster performance for implicit solvent simulations,
but PME simulations are about as fast as on a high-end CPU.
* Check-pointing is made more secure:MD5sum are used to verify
that all files are correctly in-place before a simulation is
appended. Output file appending at continuation is turned on
by default.
* Increased tolerance for networked file system failures and
cluster node crashes: checkpoint handling is safer and mdrun
forces file system cache flushes during checkpoints.
* Full CMake support. After the 4.5 release we will be
switching the default build tool from autoconf to cmake,
and possibly deprecate autoconf in the future.
* Full support for seven AMBER force fields in the standard
distribution, with default Amber names. We also include the
recent Amber99sb-ildn in the distribution.
* Support for CHARMM27, including cmap for dihedrals
* Efficient Generalized-Born implicit solvent support
including the Still/HCT/OBC-models to compute the Born radii,
a novel way of tabulating the generalized Born-interaction
formula for greater speed, and optimized SSE-routines in both
single and double precision.
* Highly efficient all-vs-all assembly kernels for both vanilla
and generalized born interactions, in both single and double
precision.
* Much better support for nucleic acid simulations, including
automatic handling by pdb2gmx.
* Support for Velocity-Verlet integrators for reversible T-
and P-coupling; MTTK pressure control integrators;
Nose-Hoover chains.
* Symplectic Trotter Leap-Frog integrator for twin-range
non-bonded interactions.
* Support for Bennet acceptance ratio calculations through
direct calculation of Hamiltonian differences during the
simulation.
* File formats: All GROMACS tools can now read any VMD
supported trajectory format, without converting trajectory
first. (VMD libraries are required).
* pdb2gmx now retains the residue numbers from the input,
mdrun and all tools use these original numbers.
New tools
* g_bar: Bennett acceptance ratio (BAR) free energy calculations,
including automatic error estimates and phase space overlap
measures.
* g_rdf was a little bit enhanced that structure factors can
be calculated for any system, by supplying the necessary data
via sfactor.dat. Most of the common atomtypes are already
contained, but everybody who needs more freedom can enhance
the table
* g_select: Library support for "dynamic index groups" based
on textual selections (experimental feature).
See the tool g_select, the included template.c, or Doxygen
documentation for information on how to write analysis tools
using the library. Existing tools have not (yet) been
converted.
* g_tune_pme: For a given number of processes or threads this
tool systematically times mdrun with various numbers of
PME-only nodes and determines which setting is fastest. It
also checks whether performance can be enhanced by shifting
load between the real and the reciprocal space part of the
Ewald sum.
* g_membed: a very convenient utility for rapidly embedding
membrane proteins into equilibrated lipid bilayers
* g_pme_error: estimates the error of the electrostatic forces
if using the SPME algorithm. TO be incorporated in g_tune_pme
Changes that might affect your results
* grompp by default sets the new nstcalcenergy parameter equal
to nstlist, this has no effect on the integration, only on
the energy averages stored in ener.edr
* grompp by default sets the new nsttcouple parameter equal to
nstlist, this means T-coupling is done less frequently;
grompp checks if tau_t is large enough
* grompp by default sets the new nstpcouple parameter equal to
nstlist, this means P-coupling is done less frequently;
grompp checks if tau_p is large enough
* mdrun results with old tpr files with twin-range non-bonded
interactions will be different, because of the new symplectic
integrator
* for free-energy calculations sc-sigma now also sets the minimum
soft-core sigma (old tpr files retain the old behavior,
which can be enforced by setting the env.var. GMX_SCSIGMA_MIN to 0)
to trigger/signal a rebuild for the transition 5.10.1 -> 5.12.1.
The list of packages is computed by finding all packages which end
up having either of PERL5_USE_PACKLIST, BUILDLINK_API_DEPENDS.perl,
or PERL5_PACKLIST defined in their make setup (tested via
"make show-vars VARNAMES=..."), minus the packages updated after
the perl package update.
sno@ was right after all, obache@ kindly asked and he@ led the
way. Thanks!
Based on PR#43388 by Wen Heping.
version 3.69 (September, 2009)
* If there are more than about 50 species in the tree, Treedist can
fail to compute distances among the trees. This is due to an overflow
problem inadvertently introduced in version 3.68. There is no
workaround with the 3.68 executable, but if you can recompile you can
fix it by replacing line 1179 of treedist.c, which is currently
maxgrp = pow(2,tip_count);
by
maxgrp = 100000;
This is fixed in version 3.69. Versions prior to 3.68 will not have
this problem.
* In Dnacomp, Pars, and Dollop, if the Shimodaira-Hasegawa test is
performed and there are trees perfectly tied with the best tree, the
P values were incorrect (being 0 instead of 1).
* A team from Iowa State University noticed that time was being wasted
in calculations in Dnapenny in the bound calculations. This has now
been remedied and it should be noticeably faster.
* In the molecular likelihood programs, ancestral state probabilities
were being incorrectly calculated for user trees that had internal
multifurcations. This has been corrected.
version 3.68 (August, 2008)
* We received some reports that Dnaml was freezing on some data sets in
the Windows executables. This seems to have been because of incorrect
handling of small increases in the log-likelihood, causing the
algorithm to fall into loops. It was temporarily cured in version 3.67
by changing the compiler optimization level, downwards from -O3 to
-O1. Now the underlying problem of small differences of log-likelihood
has been addressed too, so you should use the new Windows executables
(3.68) to avoid having these problems on Windows systems.
* We found that the .DMG (disk image) archive for Mac OS X contained
executables for the Intel Mac but not universal binaries that would
work on both Intel Mac and PowerPC systems. Oops. We recompiled and
reposted the archives (on 23 August 2007). They should work on both
kinds of systems now.
* We were told that on a Linux computer with a 64-bit Intel Itanium chip
the bootstrapping program Seqboot creates blatantly wrong bootstrap
samples with characters sampled too many times (or none). On a 64-bit
AMD processor the program works fine. The problem is in the random
number function "randum" in phylip.c. It seems to be a problem with
optimization on the GCC compiler. It is cured by dropping the compiler
optimization level from -O3 to -O2.
* In Protdist the program would blow up if it computes a distance
greater than 100.0. This is owing to a subscript error in the code
that writes out the distances, in line 1874 where
else if (d[j][k] < 1000.0)
should have been
else if (d[i][j-1] < 1000.0)
If you have this problem and cannot upgrade to version 3.68 or
recompile the program with this change, and your data comes from
bootstrapping, try omitting just that replicate, or else rerunning
the bootstrapping with a different random number seed (which might not
happen to drop as many of the sites that caused these two sequences to
be so distant).
* When Dnadist is used and the lower-triangular output format is chosen,
the resulting file has headers at the top of columns and is human-
readable but is not machine readable. The (temporary) solution is not
to use this option for the time being.
* In Mac OS X, Drawgram produces some alarming lines of text at the top
of its terminal window when it first runs. These are just scripting
commands that were not erased because we do not clear the screen at
the right moment. The workaround is simply to ignore these commands.
version 3.67 (July, 2007)
* We had our first reports on the behavior of PHYLIP Windows executables
on Windows Vista. The programs work fine. The only thing that did not
work is the self-extraction program that unpacks the archives. For
some reason it did not work on Vista. The work-around was that, after
you got an archive file like phylipwx.exe onto your system, you had to
change the file extension from "exe" to "zip". Then you had to click
on the file. You were presented with options including "Extract all
files". If you chose that the archive was unpacked. The programs would
then work. Although we provided "zip" archive versions of the package,
we have now got a new version of WinZip which is supposed to have a
self-extractor that works on Windows Vista, and it was used to produce
the self-extracting archive since 27 August 2007.
* On Mac OS X systems, if our distributed executables are placed in a
folder whose path contains a name with an internal blank, such as
/Users/ianr/the files/ then the script that causes each of our
programs to run when you click on the corresponding icon does not
work, and there is an error message. This is a scripting error in our
Mac OS X setup, and it was corrected in version 3.67. In the meantime,
if you have this problem, the solution is to put PHYLIP in a folder
whose path does not have any folder that has a blank in its name. In
the above example, all that would be necessary is to rename the folder
the files to the_files
* We are still getting reports of stickiness of the tree, and
occasionally of negative branch lengths, in Dnamlk and Promlk which
do not do as good a job of searching for best trees as they should.
This has turned out to be an issue of nodes getting stuck when they
collide in moving them on the "time" scale. Some major changes were in
the code in the 3.67 release to eliminate this stickiness and give a
good search.
* An error was made in putting together the matrices for the PAM
mutation model in Protdist, Proml, and Promlk. These programs will
give PAM calculations inconsistent with earlier (v3.65 and before)
versions, and with other programs. The matrices were corrected in
version 3.67. This does not affect JTT or PMB models.
* The W (within-species varation) option of CONTRAST uses somewhat
incorrect equations to infer within-species covariances and
phylogenetic covariances. These were corrected in version 3.67.
Anyone severely impacted by the problem in the meantime should contact
me.
* Protdist sometimes results in distances greater than or equal to
100.000. When this happens, the distance can run together with the
previous number in the output file. For example, a distance of 0.31766
followed by one which is 127.43986 might look like this:
"0.31766127.43986". This causes trouble in any program that tries to
use this distance matrix. One symptom of this may be the program
reporting that two distances which are expected to be equal are
unequal -- but then printing them both out, and they appear to be
equal! In this case it would print out a message warning you that
0.31766 was not equal to 0.31766. It is doing so because one of them
is actually seen by it as 0.31766127 and the other 0.31766. In all
future versions, there will be a blank printed between the two
numbers. For the present, use an editor to find them and insert the
blank by hand. If this is difficult, a Sed script (which can be used
on Linux or Unix machines) has been written by Doug Scofield, and is
available from him at: this link. Many thanks to him for this. As you
can see, this problem is the result of us not thinking of what happens
when the distances are big, and the fix in the code is trivial -- just
ensuring that there is at least one blank between successive
distances.
* Contml, with gene frequencies, has a bug in the transformation to
variables that have approximate Brownian motion as their evolutionary
process. This can lead to wierd trees. It might be preferable to go
back to the 3.5c version if you need to use Contml for this. We
believe that this will be correctly fixed in the 3.67 version. If
people can recompile the source code, they replace the function
transformgfs with this one and recompile (you should be able to save
it from your browser using the Save As choice in its File menu.
version 3.66 (August, 2006)
* Program Treedist was found to compute the Branch Score Distance
incorrectly. It will, in most cases, get the branch lengths in
terminal branches incorrect and then be likely to find a nonzero
distance between trees when they are really identical, and incorrect
distances when they are not identical. Alas, there is no workaround to
avoid this. All distances done with this option before version 3.66
should be regarded as incorrect unless all terminal branches have the
same length, or unless the order of species in the tree is the same as
in the first tree in the file. The Symmetric Difference option, which
does not use branch lengths, works properly.
* Program Dnamlk, when run on Linux or Windows systems, sometimes gave
negative branch lengths for some branches on the tree. This is bad.
Although we at first thought that this was a compiler bug, it seems to
be a lack of initialization of some pointers. Program Promlk may have
the same problem, as they share code. If you have this problem you can
work around it by not using the Global menu option when running Dnamlk
(or Promlk). If you need more extensive tree search the J (Jumble)
option may be your best bet.
* On Windows (at least, on Windows xp), our executables for version 3.65
produce output files (outfile) and output tree files (outtree) that
have end-of-line characters that result in their being hard to read on
the Notepad editor. They appear as one big line. If you use the
Wordpad editor, or Microsoft Word itself, the files will be readable.
This is and end-of-line compiler setting we got wrong when compiling
the programs.
* Programs Dnaml and Proml sometimes failed to iterate branch lengths in
trees enough -- this can result in them failing to find as good a tree
as the molecular clock versions Dnamlk and Promlk, a phenomenon that
is not supposed to occur. The problem results from the iteration code
in function makenewv giving up too easily when branch lengths are very
short. The resulting branches get "stuck" at length 0 when they should
not. If you can recompile the programs, the problem can be solved by
the following changes:
o In file phylip.h change the value of the constant iterations to
8 instead of 4.
o In files dnaml.c and proml.c, change function makenewv to
replace
done = fabs(y-yold) < epsilon;
by
done = fabs(y-yold) < 0.1*epsilon;
o In dnaml.c, in function makenewv, also replace*
if (yold < epsilon)
yold = epsilon;
by
if (y < epsilon)
y = epsilon;
We think these fix the problem. Some more thorough fixes are
implemented in the 3.66 code.
* The Mac OS X archives (in .dmg form) appeared at first sight not to
have any executables directory in the package. This is owing to
strange placement of icons once we package the files. The OS X
executables are there -- their folder is just way down the window. Use
the scroll bar to look for them. You should be able to use the
View/Rearrange menus to make the folder icons appear in a more
reasonable place. (Or this can be done once all of the contents of the
.dmg archive are copied out to another folder).
* Programs Dnaml and Proml (but not Dnamlk or Promlk), from version 3.64
on, crashed if the Categories (C) option is used, even if all
categories are given the same rate of change. This unpleasant behavior
does not occur if the menu option for "Speedier but rougher analysis"
is changed to "No, not rough". That slows down the run but allows it
to succeed.
The fix turns out to be that all instances in dnaml.c of calls to
function copynode (or all instances in proml.c of calls to
prot_copynode) that involve an argument lrsaves should have the third
argument be rcategs instead of categs.
* In Seqboot, when menu item J is set to Permute species within
characters it is impossible to change menu item W (character weights).
This is a glitch in the menuing code. If you can change the source
code and recompile, change at line 215 of seqboot.c:
((permute || ild || lockhart)
&& (strchr("ACDEFSJPRXNI%1.20",ch) != NULL)) ||
to be:
(permute && (strchr("ACDEFSJPRWXNI%1.20",ch) != NULL)) ||
((ild || lockhart) && (strchr("ACDEFSJPRXNI%1.20",ch) != NULL)) ||
If you are stuck with our executables and need this feature, you can
also work around it in the following devious way:
1. Set menu item J to some other setting where menu item W appears
in the menu, such as Bootstrap,
2. Change menu item W
3. Then change item J to Permute species within characters
4. Our Makefile for Unix had some problem finding some of the
X-windows libraries on Mac OS X systems on Intel Macs. This
prevented the compilation of Drawtree and Drawgram. You might
have had to use those two programs by using their PowerMac Mac
OS X executables. All the other programs did compile and run
correctly on Intel Macs.
version 3.65 (August, 2005)
* Protpars sometimes gave the result "0 trees found" or else simply
hung and did not complete its run. This was a bug. The program should
always get at least one tree -- if it does not, that is a bug and not
a judgement on your data, provided the data file is in our format!
* Proml and Restml, and maybe some others, seg-faulted when run on
enough multiple data sets, as in bootstrapping. If you have a version
that has this problem and can recompile the programs, here is a fix
for Proml and Restml. In function "inputdata", replace the lines
makeweights();
if ( firstset ) alloclrsaves();
else resetlrsaves();
by
if ( !firstset ) freelrsaves();
makeweights();
alloclrsaves();
and you can also eliminate the now-unnecessary function "restlrsaves".
(Thanks to Jacques Rougemont for this).
version 3.64 (July, 2005)
* Treedist had trouble on Windows systems reading trees. This was due to
problems with the ftell command on CygWin. It has been fixed by having
the files read as binary files.
* Trees with branch lengths compared using Treedist may have incorrect
distances when evaluated as unrooted trees, owing to miscalculation of
branch lengths for the bottommost branches.
* Runs of Seqboot on Mac OS X systems with gene frequencies data have
showed incorrect results -- wrong numbers of loci sampled, for
example. This is due to bad code generated by the Metrowerks
Codewarrior compiler when set to higher levels of optimization (our
source code is OK). We will recompile the program at a lower level of
optimization in the next bug-fixing release. If you can follow our
compiling instructions and have this compiler, you can produce a
correctly working executable. Alternatively you can use the gcc
compiler and use our Unix Makefile to recompile this program (by
typing "make seqboot"). This is quite easy to do and all Mac OS X
releases have the gcc compiler in them -- it only needs to be
installed.
* In runs of Proml, Dnaml or Restml with user trees, if one puts in a
user tree with an internal multifurcation and asks the program to re-
estimate the branch lengths for that tree, the branch lengths in only
two of the furcs will be re-estimated if they already have branch
lengths. This is due to a bug in the function "initrav" causing it to
fail to enter one or more of the subtrees. A workaround until the next
release is as follows: Use Retree to remove all branch lengths on the
tree. The tree's branch lengths will then all be re-estimated when it
is used as a user tree.
* The example output in the Treedist documentation gives distances
computed by version 3.62 or earlier, in which the tree distance is not
square-rooted.
version 3.63 (December, 2004)
* The DNA and protein likelihood programs could have problems with
underflow if very large numbers of sequences were analyzed. Underflow
protection code was needed to make this much less likely to happen.
* A number of programs had the problem that when M (multiple data set)
runs are done, if the data sets differ in the number of characters
from data set to data set, they only allocate enough memory for the
first data set, and then can crash on subsequent, larger, data sets.
For bootstrap and permutation runs this should not be a problem, but
for jackknife runs it might be. One work-around until we fixed this
was to move the data set with the most characters to the front, so
that enough space is allocated. The programs we think had this problem
are: Clique, Dnacomp, Proml, Promlk, Protdist, Dollop, Gendist, Pars,
Restml, and Restdist.
* When the Branch Score distances are computed in program Treedist, the
sum of squares of differences between branches was not square-rooted,
as the documentation web page says it is.
* Fitch and Contml may die when asked to do Jumbling, in some cases.
* Dnaml had inconsistencies in results when branch lengths of a user
tree were estimated, and when the same numbers were provided in the
user tree.
* Trees fed into Contrast could cause trouble if they contained
unifurcations (forks with only one descendant). The program did not
complain about this, as it should have.
* End-of-line characters in input files in certain cases caused trouble
in Mac OS X (for example when the files came over from Windows).
* When printing a rooted tree out in Kitsch, the root was not placed
intermediate between its two decsendants.
* The variable numtrees was sometimes used when still uninitialized in
Pars.
* Restdist had a site-aliasing bookkeeping bug that could lead to
incorrect results.
* Restml would not allow site lengths greater than 8, because an array
was of fixed size when it should have been dynamically allocated.
* The variable name howmany conflicts with predefined names in some
older Sun compilers. It will henceforth be deliberately misspelled to
avoid this.
* With larger data sets being analyzed, Proml, Promlk, Dnaml, and
Dnamlk have had to have underflow protection code installed, as
likelihoods were getting too small.
* Treedist was giving wrong answers when asked to compute all distances
between trees in two files that had unequal numbers of trees. This
was a bookkeeping error.
* The variable scanned was uninitialized in the Drawtree and Drawgram
programs, which could sometimes cause problems.
* The lack of initialization of a variable, delta in Dnadist meant that
different results could be obtained from interactive runs than were
obtained in runs under the control of a command file.
* Dnadist was sometimes stopping when encountering sequences that had
an infinite or indeterminate distance (i.e. when the sequences were
too different or when they had no sites in common), when it should
have printed out "-1" and continued. When it was supposed to print
"-1" in some recent versions of PHYLIP it printed "1.0000" instead.
version 3.62 (September, 2004)
* The ftp link used by our "Get Me PHYLIP" page to fetch the version
3.62 Linux gzip'ed sources and documentation archive was incorrect
until recently (I hadn't updated it to fetch version 3.62). If you had
trouble fetching this archive in version 3.62, please try one more
time. It will work now.
* A number of people have found, with Fitch and with Contml, that
version 3.61 crashes on multiple Jumbling (option J) or on bootstrap
runs. This is fairly serious. It does not happen with versions of
these programs earlier than 3.6 (such as 3.6a3 or 3.573c). This
release fixes these problems.
From pkgsrc-wip, packaged originally by Peter Ibsen Hansen.
GROMACS is a versatile package to perform molecular dynamics,
i.e. simulate the Newtonian equations of motion for systems with
hundreds to millions of particles.
Changes since previous package:
Chemtool-1.6.12 (June 7, 2009)
This release contains another round of fixes for label positioning
and clipping of bonds around labels. The pen color button has been
replaced by a drop-down menu, and a "white" pen for drawing on
colored backgrounds has been added. Chemtool now automatically
resizes its main window on small (netbook) screens, and it can also
be used in an non-interactive mode to create postscript (etc.) output
from previously created chemtool structure files. The Polish
translation has been updated, and a new Bulgarian translation
has been added.
Chemtool-1.6.11 (August 26, 2007)
This release contains numerous fixes for label positioning and
sub/superscript kerning. Bond length and zoom factor are now
stored with the drawing, bond clipping of multiple bonds was
improved and new special key sequences for circled plus and
minus symbols were added. The configuration dialog now lists
gtklp among the supported print commands. Source layout and
build system were reorganized to make addition of translations
easier, and a Portuguese localization file was added.
Chemtool-1.6.10 (April 8th, 2007)
This release adds PNG export, round brackets, text output in
east-european locales and some new templates. Several bugs
related to special character handling in GTK2, screen display
of labels and exporting to EPS and SVG have been fixed. The
configuration dialog has been redone and now includes support
for kprinter, and the labeling shortcuts no longer interfere
with GTK's menu accelerators.
Changes: This release adds a feature that can automatically choose
food quantities when a meal is to have a particular amount of fat,
protein, or carbohydrate. Currently, you can modify a food quantity
from the meal list by typing the food number and a new quantity.
For example, "2 100g" means change food #2 to 100 grams. This
feature allows the user to type "protein", "carb", or "fat" instead
of an explicit new quantity. For example, "2 carb" indicates that
you want the second food's quantity changed so that the meal's
Daily Value for non-fiber carb is satisfied.
* 14.3
Changes: This release modifies the default polyunsaturated fat
reference values.
* 14.2
Changes: This release revises the default fatty acid reference
values.
* 14.1
Changes: This release updates the Omega-3 defaults.
* 14.0
Changes: This release introduces the new USDA Nutrient Database
SR21, and allows current nut installations to have their existing
meal records reinterpreted with the new database.
Shared directories can now be created independently by the pacakges
needing them and will be removed automatically by pkg_delete when empty.
Packages needing empty directories can use the @pkgdir command in PLIST.
Discussed and ok'd in thread starting at
http://mail-index.netbsd.org/tech-pkg/2009/06/30/msg003546.html
on some platforms that lacked shared library support in the past. The
list hasn't been maintained at all and the gain is very limited, so just
get rid of it.
to trigger/signal a rebuild for the transition 5.8.8 -> 5.10.0.
The list of packages is computed by finding all packages which end
up having either of PERL5_USE_PACKLIST, BUILDLINK_API_DEPENDS.perl,
or PERL5_PACKLIST defined in their make setup (tested via
"make show-vars VARNAMES=...").
patches to add it). Drop pax from the default USE_TOOLS list.
Make bsdtar the default for those places that wanted gtar to extract
long links etc, as bsdtar can be built of the tree.
- assume that Python 2.4 and 2.5 are compatible and allow checking for
fallout.
- remove PYTHON_VERSIONS_COMPATIBLE that are obsoleted by the 2.3+
default. Modify the others to deal with the removals.
Pkgsrc changes:
Add DESTDIR support.
Recent changes (cannot available changes from 10.18 to 12.6 anymore).
13.2:
This release makes minor changes to the analysis reset and food suggestion
functions.
13.1:
This release changes some fatty acid defaults to allow more saturated fat when
eating low-carb, and to raise the maximum amount of long-chain Omega-3.
13.0:
This release introduces the new USDA Nutrient Database SR20 and allows current
NUT installations to have their existing meal records reinterpreted with the new
database.
12.7:
This release uses a new food name abbreviation algorithm so that food names are
more informative and less cryptic.
INSTALLATION_DIRS, as well as all occurrences of ${PREFIX}/man with
${PREFIX}/${PKGMANDIR}.
Fixes PR 35265, although I did not use the patch provided therein.
PKGLOCALEDIR and which install their locale files directly under
${PREFIX}/${PKGLOCALEDIR} and sort the PLIST file entries. From now
on, pkgsrc/mk/plist/plist-locale.awk will automatically handle
transforming the PLIST to refer to the correct locale directory.
developer is officially maintaining the package.
The rationale for changing this from "tech-pkg" to "pkgsrc-users" is
that it implies that any user can try to maintain the package (by
submitting patches to the mailing list). Since the folks most likely
to care about the package are the folks that want to use it or are
already using it, this would leverage the energy of users who aren't
developers.
This release fixes a bug i(crash on startup) that was exposed by gcc 4.
It also adds detection of the recently released OpenBabel 2.0 and the ability
to use Openbabel for exporting to foreign file formats. Subscript encoding in
the SVG export was tweaked again to work around current limitations in the SVG
support of Firefox 1.5 and Konqueror 3.x.
of main. Why does it have to be int? Well, not returning anything can
result in a random exit code. Add make(1) as caller and the normal
behaviour of just stopping on the first error and this package has
a very low success rate for building e.g. on DragonFly.
- Fixed several serious bugs related to label rendering and printing
that occured when chemtool was built with GTK 2 instead of GTK 1.2
(see ChangeLog for details)
- SVG export now adds a namespace header as required by current builds
of the firefox browser
- SVG export now uses color values instead of color names for better
SVGT compatibility
- The separation between the lines of multiple bonds is configurable
- The keys of the numeric keypad now create two dots instead of a line
for free electron pairs when the Shift key is pressed
- Two new bond types for drawing filled and unfilled p orbital lobes
- chemtool now checks for fig2sxd (sourceforge.net) and offers to export
to OpenOffice Draw format when it is present.
- rpm packages did not install the dutch locale file.
Chnges 1.6.6:
- Fixed bug in molfile preview that caused an immediate crash in 1.6.5
- Made drawing of wiggly bonds work again
Several changes are involved since they are all interrelated. These
changes affect about 1000 files.
The first major change is rewriting bsd.builtin.mk as well as all of
the builtin.mk files to follow the new example in bsd.builtin.mk.
The loop to include all of the builtin.mk files needed by the package
is moved from bsd.builtin.mk and into bsd.buildlink3.mk. bsd.builtin.mk
is now included by each of the individual builtin.mk files and provides
some common logic for all of the builtin.mk files. Currently, this
includes the computation for whether the native or pkgsrc version of
the package is preferred. This causes USE_BUILTIN.* to be correctly
set when one builtin.mk file includes another.
The second major change is teach the builtin.mk files to consider
files under ${LOCALBASE} to be from pkgsrc-controlled packages. Most
of the builtin.mk files test for the presence of built-in software by
checking for the existence of certain files, e.g. <pthread.h>, and we
now assume that if that file is under ${LOCALBASE}, then it must be
from pkgsrc. This modification is a nod toward LOCALBASE=/usr. The
exceptions to this new check are the X11 distribution packages, which
are handled specially as noted below.
The third major change is providing builtin.mk and version.mk files
for each of the X11 distribution packages in pkgsrc. The builtin.mk
file can detect whether the native X11 distribution is the same as
the one provided by pkgsrc, and the version.mk file computes the
version of the X11 distribution package, whether it's built-in or not.
The fourth major change is that the buildlink3.mk files for X11 packages
that install parts which are part of X11 distribution packages, e.g.
Xpm, Xcursor, etc., now use imake to query the X11 distribution for
whether the software is already provided by the X11 distribution.
This is more accurate than grepping for a symbol name in the imake
config files. Using imake required sprinkling various builtin-imake.mk
helper files into pkgsrc directories. These files are used as input
to imake since imake can't use stdin for that purpose.
The fifth major change is in how packages note that they use X11.
Instead of setting USE_X11, package Makefiles should now include
x11.buildlink3.mk instead. This causes the X11 package buildlink3
and builtin logic to be executed at the correct place for buildlink3.mk
and builtin.mk files that previously set USE_X11, and fixes packages
that relied on buildlink3.mk files to implicitly note that X11 is
needed. Package buildlink3.mk should also include x11.buildlink3.mk
when linking against the package libraries requires also linking
against the X11 libraries. Where it was obvious, redundant inclusions
of x11.buildlink3.mk have been removed.
10.18:
This release contains a fix for the floating point
exception on NetBSD-2.0/alpha.
10.17:
This release corrects the formatting of the man page and
restores the correct alpha-linolenic acid reference
value, which was too low in the last release.
10.16:
This release fixes a segfault that occurs when analyzing
added and subtracted foods that total zero calories.
10.15:
This release completes the changing of all calculations
to substitute user averages for program constants in the
values of calories per gram of carb, fat, and protein,
and of the percentage of total fat that is fatty acids.
This means that personal options in terms of percentages
and ratios will be more precise.
