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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 !!! @ text @@@comment $NetBSD: PLIST,v 1.3 2009/06/14 17:34:34 joerg Exp $ bin/ppuzzle bin/puzzle share/doc/puzzle/tree-puzzle.pdf share/examples/puzzle/EF.3trees share/examples/puzzle/EF.phy share/examples/puzzle/atp6.a share/examples/puzzle/globin.a share/examples/puzzle/marswolf.n share/examples/puzzle/primates.b @ 1.3 log @Remove @@dirrm entries from PLISTs @ text @d1 1 a1 1 @@comment $NetBSD: PLIST,v 1.2 2003/05/10 23:46:15 jtb Exp $ a3 3 share/doc/html/puzzle/ppuzzle.gif share/doc/html/puzzle/puzzle.gif share/doc/html/puzzle/tree-puzzle.html @ 1.2 log @Update to version 5.1. Many minor enhancements and bugfixes. Manual updated. @ text @d1 1 a1 1 @@comment $NetBSD: PLIST,v 1.1 2001/10/31 21:28:12 zuntum Exp $ a13 3 @@dirrm share/doc/puzzle @@dirrm share/doc/html/puzzle @@dirrm share/examples/puzzle @ 1.1 log @Move pkg/ files into package's toplevel directory @ text @d1 1 a1 1 @@comment $NetBSD: PLIST,v 1.2 2001/07/08 13:36:34 jtb Exp $ d4 6 a9 3 share/doc/puzzle/manual.html share/doc/puzzle/ppuzzle.gif share/doc/puzzle/puzzle.gif d15 1 @