2007-05-30 Ralf Westram * Makefile: - proper 'clean' 2004-04-29 Ralf Westram * doc/manual.html: - removed umlauts 2003-09-19 Ralf Westram * src/util.c: - const fix Version date what has been changed 5.0 26.08.2000 - changes to manual, Makefile.in - cpREV hidden by -DCPREV flag - chi2test, quartio included into source code files - generic scr/Makefile.generic - src/makefile.com for VAX - AUTHORS, README, ChangeLog updated - INSTALL checked 27.08.2000 - test code excluded - '-randseed#' added for debugging purposes - ./data added to autoconf/automake - warning output if cmdline parameter unknown 11.10.2000 - fixed output of rate categories of sites before computing them - check whether rate categories were computed by 1st user tree or NJ tree fixed in the output 12.10.2000 - invariant site model normalization fixed CODE FREEZE =========== 5.0.a33 15.08.2000 - changes for autoconf/automake 5.0.a32 01.08.2000 - a FPE error fixed (badq == 0) - small error in -bestq fixed - fflush's added at several places 5.0.a31 01.08.2000 - comments added to tree structure sorting puzzle2.c - changes in configure.in, Makefile.in 5.0.a30 23.07.2000 - some debugging in checkquart - changed to autoconf 5.0.a29 13.07.2000 - some debugging in checkquart 5.0.a28 13.07.2000 - use best quartet topology option (-bestq) implemented 5.0.a27 13.07.2000 - further developement to checkquart - ascii/binary quartet values (-wqla/-wqlb) - typo correction 5.0.a26 11.07.2000 - fflush at all checktimer - further developement at checkquart - possibility to write quartet values to file (-wqlh) 5.0.a25 06.07.2000 - fflush at checktimer 5.0.a24 02.07.2000 - further debugging of checkquart 5.0.a23 02.07.2000 - further developement to checkquart 5.0.a22 29.06.2000 - checkquart added to makefile - bad quartet stats added after reading in *.allquarts 5.0.a21 27.06.2000 - site pattern statistics implemented and added to SEQUENCE ALIGNMENT section in puzzle report 5.0.a20 26.06.2000 - cpREV45 implemented 5.0.a19 26.06.2000 - for debugging purposes: typo "MPE" changed to "FPE" - fflush(stdout) added in chi2test 5.0.a18 20.06.2000 - checkquart implemented 5.0.a17 19.06.2000 - FPRINTF(STDOUTFILE and STDOUT definition changed and moved; fputid/fputid10 writes to STDOUT instead of stdout - ppuzzle checks slaves enough slave-processes - numquarts, num2quart, quart2num moved from ppuzzle.c to puzzle1.c - read/writeallquart implemented (undocumented feature) to be used by -wqf/-rqf at comandline -wqf = write quartet file (infilename.allquart) after quartet evaluation -rqf = read quartet file (infilename.allquart), no quartet evaluation, unless -wqf is used as well, then quartets are written and read in - '-h' option at comandline -> printusage 5.0.a16 31.05.2000 - chi2test bug fixed - WAG matrix added, model choice adopted 13.06.2000 - date set to June 2000 - author order changed to Schmidt, Strimmer, Vingron, v.Haeseler - CPU time output stopped, due to overflow errors 16.06.2000 - sequence composition chi2test moved before parameter output. - output of chi2test and bad quartet statistics split, to do the chi2test output earlier. 5.0.a15 02.05.2000 - Names changed back from TREE-PUZZLE to PUZZLE 09.05.2000 - and to TREE-PUZZLE again ;-) 5.0.a14 13.03.2000 - Changes to the manual. - Executable names changed to (p)treepuzzle. (changes in the makefiles) 15.03.2000 - Output of parameters after estimation added. 5.0.a13 18.02.2000 - ALPHA version number removed from the code 5.0.a12 18.02.2000 - CPU time measurement problems fixed for case where clock_t is an unsigned type. 5.0.a11 17.02.2000 - time measure problems (CPU/wallclock) fixed not all features in addtimes are used at the moment. - unnecessary and unused routines removed fron source code. 5.0.a10 20.01.2000 - Name changes from PUZZLE to TREE-PUZZLE - Chi2-fit model guessing for VT model added - little model printing bug fixed 5.0.a9 22.12.1999 - VT Model incorporated (Mueller, Vingron (2000) JCB, to appear). - TODO: Chi2-fit model guessing for VT model 5.0.a8 21.12.1999 - 'sys/times.h' and 'sys/types.h' removed from puzzle.h. They were neither ANSI conform nor necessary, but occured in the SUN man pages. - Definition and call of writetimesstat eliminated from the sequention version by compiler switched, and not just the function body as before. - '-O4' canged to '-O' to be more generic. 5.0.a7 21.12.1999 - Macro constants introduced for data_optn (NUCLEOTIDE, AMINOACID, BINARY) - round robbing of datatype and AA model option changed in menu to make adjustment of the model possible by a determined sequence of letters: 'd': Auto -> Nucleotides -> Amino acids -> Binary states -> Auto ('m' && data_optn == AMINOACID): Auto -> Dayhoff -> JTT -> mtREV24 -> BLOSUM62 -> Auto - manual.html adjusted 5.0.a6 20.12.1999 - new manual.html added 5.0.a5 07.12.1999 - output bug fixed (bestrates were written before they were computed) 5.0.a4 02.12.1999 - header file inclusion ajusted: added: #include changed from: #include "ppuzzle.h" to: #ifdef PARALLEL # include "ppuzzle.h" #endif 5.0.a3 27.11.1999 - '-h' comandline option removed, because of problems with MPICH under LINUX - new memory leaks of 5.0.a2 closed in PP_Finalize 5.0.a2 27.11.1999 - Cleanup of the source code - Measurement of CPU time added - Parallel load statistics added (quartets, trees, time) to puzzle report. - Cleanup debug messages - Comments "[...]" are removed from usertrees now. - single quotes will only be printed arount species names if -DUSEQUOTES is set at compiletime. - tree likelihood is printed infront of a tree as a comment, [ lh=-xx.xxxxx ](...); 5.0.a1 26.11.1999 - Cleanup of the directories - Copyright changes - Version changes VERSION CHANGE ============== 4.1.a26 25.11.1999 - Makefile made universal for pauzzle and ppuzzle - lines not needed removed from puzzle.h 4.1.a25 19.11.1999 - Output file prefixes for distances, trees, and puzzlereport changed in user trees analysis case to user tree file name - Temporary output of likelihood to treefile added 4.1.a24 11.11.1999 - Output of puzzling step trees changed ptorder: [ orderno # % ID #UniqTopos #Steps ]PHYLIP pstep: chunk #InChunk sum ID #UniqTopos #Steps - preliminary leap frog RNG implemented, i.e. uses the rand4 in the usual way in the sequential case. If run in parallel all rand4 are initialized with the same seed and started with PP_Myid-th random number. after that each process uses the every PP_NumProcs-th random number to make sure that these unique. 4.1.a23 08.11.1999 - output of sequential and parallel version to *.pstep made identical 4.1.a22 05.11.1999 - two different puzzle step tree outputs intruduced and added to the menu ("[ 1. 35 ](...);": - ordered unique tree list -> *.ptorder Format: "[ 1. 35 ]" (Ordernumber, Amount) - chronological tree list -> *.pstep Format: "[ 1. 35 ]" (Chunknumber, Amount in chunk) (the last is a problem in parallel, because the come in chunks, as scheduled) - debugged the output 4.1.a21 04.11.1999 - Makefile adjustments for other Plattforms - pstep tree output changed. unique treestructures printed to *.pstep file with a leading comment containing an order number and the ammount padded with blanks (e.g. "[ 1. 356 ]('mouse'..."). output is done right before writing the puzzle file. - controlled MPI finish to the Quit menu option added 4.1.a20 03.11.1999 - some garbage collection (free) added - makefile adjusted, OFLAGS for optimization added (ppuzzle/MPICH has problems with -O, so the ppuzzle is created without optimization) Some minor changes in the makefiles - still to do: garbage collection from 'internalnode' in master process 4.1.a19 13.10.1999 - adding the output of standardized (i.e. sorted) puzzling step trees. Those are printed to the standard output at the moment. (Routines to sort and print the trees implemented) 14.10.1999 - routines for printing the sorted trees to a string. needed to send them between Master and Worker, and to have a unique key to sort and count the trees. 21.10.1999 - counting of sorted trees implemented by doubly linked list, sort routine, print to stdout 25.10.1999 - change place of writing distances to file right after distances have been computed. - output of puzzling step trees now with true name, not numbers 02.11.1999 - parallel counting and sending of puzzling step trees - some parallel sending bugs fixed 4.1.a18 14.09.1999 - adding possibility to specify input file at command line, this specifies also the output filenames (puzzle output: *.puzzle; treefile: *.tree; distances: *.dist; Triangel EPS: *.eps; unresolved: *.qlist; puzzling step trees: *.pstep) If an unexisting name is given, one has to reenter the right name, but the wrong one is used as prefix. 15.09.1999 - sending back of bad quartets from slaves added - bug in quart2num fixed (not used before; was shifted by 1) - first version of a README added ;-) 4.1.a17 03.08.1999 - Recv-Error in receiving DoPuzzleBlock fixed - double freeing of same MPI_Datatype fixed - changing of scheduling algorithm to smaller chunks in gss -> sgss 13.09.1999 - bug fixed in optimization routine in ml2.c: boundary check added 4.1.a16 12.07.1999 - slight changes in verbosity levels - changed all printf to FPRINTF(STDOUTFILE to change easily from stdout to a file. 4.1.a15 08.07.1999 - scheduler for both parallel parts - several small changes 4.1.a14 25.06.1999 - computation of tree parallel, scheduler dependent, sending all biparts in one message instead of one by one - several small changes since a13 in sched.c, et al. 4.1.a13 10.06.1999 - computation of tree parallel (chunk = #trees/#slaves) - scheduling schemes implemented for minimum chunk sizes 4.1.a12 07.06.1999 - computation of quartets properly parallel - scheduling implemented - counting of quartets by slave ajusted - TODO: sending of bad quartets (array + list) - distinction between '1st user tree' and 'NJ tree' in result output removed again 4.1.a11 28.05.1999 - PP_SendDoQuartBlock, PP_RecvDoQuartBlock, PP_SendQuartBlock, PP_RecvQuartBlock - mallocquartets() changed from global to local variables to be more flexible - Quartet computation moved to slave (badquartet handling missing: output, badquartet vector); - distinction between '1st user tree' and 'NJ tree' added in result output (puzzle1.c around l.1756) 4.1.a10 20.05.1999 - num2quart, numquarts, quart2num introduced - parallel init/finalize, quartets computed on master and slave, compared -> equal -> all necessary parameter exported 4.1.a9 19.05.1999 - 'dvector forg' removed from onepamratematrix cmdline, because it's not used in the function. 4.1.a8 18.05.1999 - add _GAMMA_ (not necessary) to gamma.h and _PUZZLE_ to puzzle.h to avoid dublicate includes, possible due to ppuzzle.h - ppuzzle added to makefile and to check - 1st parallel version but no slave computations only sending parameters and done signals. 4.1.a7 18.05.1999 - export reevaluation of tree and evaluation of usertrees to evaluatetree. 4.1.a6 17.05.1999 - -DNEWFORLOOP added to fixed.src, because the changed for loop structure changes the sequence of randomized quartets during likelihood mapping - change 'int main()' to 'int main(argc, argv)' - export more functionalities from main: memcleanup(), inputandinit(&argc, &argv) - grouping if's (excluding eachother) together in switch() - split treereavaluation and 1st usertree, evaluate all usertrees together (TODO: both, treereavaluation and usertrees in one loop) - MAKE CHECK added to ./makefile 4.1.a5 16.05.1999 - adding ´dvector Brnlength´ to lslength cmdline to reduce globality of Brnlength. (Later better to *Tree) 4.1.a4 11.05.1999 - structure of for loops changed in computeallquartets and recon_tree, so that the quarted addresses are in one contigous sequence (for a