| 1 | 2007-05-30 Ralf Westram <westram@bio.tum.de> |
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| 2 | |
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| 3 | * Makefile: - proper 'clean' |
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| 4 | |
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| 5 | 2004-04-29 Ralf Westram <Coder@ReallySoft.de> |
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| 6 | |
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| 7 | * doc/manual.html: - removed umlauts |
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| 8 | |
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| 9 | 2003-09-19 Ralf Westram <Coder@ReallySoft.de> |
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| 10 | |
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| 11 | * src/util.c: - const fix |
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| 12 | |
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| 13 | Version date what has been changed |
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| 14 | |
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| 15 | 5.0 26.08.2000 - changes to manual, Makefile.in |
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| 16 | - cpREV hidden by -DCPREV flag |
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| 17 | - chi2test, quartio included into source code files |
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| 18 | - generic scr/Makefile.generic |
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| 19 | - src/makefile.com for VAX |
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| 20 | - AUTHORS, README, ChangeLog updated |
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| 21 | - INSTALL checked |
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| 22 | 27.08.2000 - test code excluded |
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| 23 | - '-randseed#' added for debugging purposes |
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| 24 | - ./data added to autoconf/automake |
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| 25 | - warning output if cmdline parameter unknown |
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| 26 | 11.10.2000 - fixed output of rate categories of sites before |
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| 27 | computing them |
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| 28 | - check whether rate categories were computed by |
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| 29 | 1st user tree or NJ tree fixed in the output |
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| 30 | 12.10.2000 - invariant site model normalization fixed |
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| 31 | |
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| 32 | |
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| 33 | CODE FREEZE |
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| 34 | =========== |
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| 35 | |
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| 36 | 5.0.a33 15.08.2000 - changes for autoconf/automake |
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| 37 | |
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| 38 | 5.0.a32 01.08.2000 - a FPE error fixed (badq == 0) |
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| 39 | - small error in -bestq fixed |
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| 40 | - fflush's added at several places |
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| 41 | |
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| 42 | 5.0.a31 01.08.2000 - comments added to tree structure sorting puzzle2.c |
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| 43 | - changes in configure.in, Makefile.in |
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| 44 | |
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| 45 | 5.0.a30 23.07.2000 - some debugging in checkquart |
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| 46 | - changed to autoconf |
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| 47 | |
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| 48 | 5.0.a29 13.07.2000 - some debugging in checkquart |
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| 49 | |
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| 50 | 5.0.a28 13.07.2000 - use best quartet topology option (-bestq) implemented |
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| 51 | |
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| 52 | 5.0.a27 13.07.2000 - further developement to checkquart |
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| 53 | - ascii/binary quartet values (-wqla/-wqlb) |
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| 54 | - typo correction |
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| 55 | |
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| 56 | 5.0.a26 11.07.2000 - fflush at all checktimer |
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| 57 | - further developement at checkquart |
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| 58 | - possibility to write quartet values to file (-wqlh) |
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| 59 | |
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| 60 | 5.0.a25 06.07.2000 - fflush at checktimer |
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| 61 | |
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| 62 | 5.0.a24 02.07.2000 - further debugging of checkquart |
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| 63 | |
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| 64 | 5.0.a23 02.07.2000 - further developement to checkquart |
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| 65 | |
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| 66 | 5.0.a22 29.06.2000 - checkquart added to makefile |
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| 67 | - bad quartet stats added after reading in *.allquarts |
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| 68 | |
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| 69 | 5.0.a21 27.06.2000 - site pattern statistics implemented and added to |
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| 70 | SEQUENCE ALIGNMENT section in puzzle report |
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| 71 | |
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| 72 | 5.0.a20 26.06.2000 - cpREV45 implemented |
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| 73 | |
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| 74 | 5.0.a19 26.06.2000 - for debugging purposes: typo "MPE" changed to "FPE" |
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| 75 | - fflush(stdout) added in chi2test |
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| 76 | |
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| 77 | 5.0.a18 20.06.2000 - checkquart implemented |
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| 78 | |
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| 79 | 5.0.a17 19.06.2000 - FPRINTF(STDOUTFILE and STDOUT definition changed |
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| 80 | and moved; fputid/fputid10 writes to STDOUT instead |
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| 81 | of stdout |
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| 82 | - ppuzzle checks slaves enough slave-processes |
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| 83 | - numquarts, num2quart, quart2num moved from ppuzzle.c |
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| 84 | to puzzle1.c |
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| 85 | - read/writeallquart implemented (undocumented feature) |
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| 86 | to be used by -wqf/-rqf at comandline |
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| 87 | -wqf = write quartet file (infilename.allquart) after |
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| 88 | quartet evaluation |
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| 89 | -rqf = read quartet file (infilename.allquart), no |
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| 90 | quartet evaluation, unless -wqf is used as |
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| 91 | well, then quartets are written and read in |
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| 92 | - '-h' option at comandline -> printusage |
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| 93 | |
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| 94 | 5.0.a16 31.05.2000 - chi2test bug fixed |
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| 95 | - WAG matrix added, model choice adopted |
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| 96 | 13.06.2000 - date set to June 2000 |
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| 97 | - author order changed to Schmidt, Strimmer, Vingron, |
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| 98 | v.Haeseler |
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| 99 | - CPU time output stopped, due to overflow errors |
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| 100 | 16.06.2000 - sequence composition chi2test moved before |
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| 101 | parameter output. |
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| 102 | - output of chi2test and bad quartet statistics split, |
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| 103 | to do the chi2test output earlier. |
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| 104 | |
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| 105 | 5.0.a15 02.05.2000 - Names changed back from TREE-PUZZLE to PUZZLE |
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| 106 | 09.05.2000 - and to TREE-PUZZLE again ;-) |
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| 107 | |
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| 108 | 5.0.a14 13.03.2000 - Changes to the manual. |
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| 109 | - Executable names changed to (p)treepuzzle. |
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| 110 | (changes in the makefiles) |
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| 111 | 15.03.2000 - Output of parameters after estimation added. |
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| 112 | |
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| 113 | 5.0.a13 18.02.2000 - ALPHA version number removed from the code |
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| 114 | |
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| 115 | 5.0.a12 18.02.2000 - CPU time measurement problems fixed for case where |
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| 116 | clock_t is an unsigned type. |
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| 117 | |
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| 118 | 5.0.a11 17.02.2000 - time measure problems (CPU/wallclock) fixed |
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| 119 | not all features in addtimes are used at the moment. |
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| 120 | - unnecessary and unused routines removed fron source |
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| 121 | code. |
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| 122 | |
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| 123 | 5.0.a10 20.01.2000 - Name changes from PUZZLE to TREE-PUZZLE |
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| 124 | - Chi2-fit model guessing for VT model added |
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| 125 | - little model printing bug fixed |
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| 126 | |
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| 127 | 5.0.a9 22.12.1999 - VT Model incorporated (Mueller, Vingron (2000) |
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| 128 | JCB, to appear). |
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| 129 | - TODO: Chi2-fit model guessing for VT model |
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| 130 | |
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| 131 | 5.0.a8 21.12.1999 - 'sys/times.h' and 'sys/types.h' removed from |
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| 132 | puzzle.h. They were neither ANSI conform nor |
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| 133 | necessary, but occured in the SUN man pages. |
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| 134 | - Definition and call of writetimesstat eliminated |
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| 135 | from the sequention version by compiler switched, |
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| 136 | and not just the function body as before. |
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| 137 | - '-O4' canged to '-O' to be more generic. |
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| 138 | |
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| 139 | 5.0.a7 21.12.1999 - Macro constants introduced for data_optn |
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| 140 | (NUCLEOTIDE, AMINOACID, BINARY) |
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| 141 | - round robbing of datatype and AA model option changed |
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| 142 | in menu to make adjustment of the model possible by a |
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| 143 | determined sequence of letters: |
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| 144 | 'd': Auto -> Nucleotides |
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| 145 | -> Amino acids |
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| 146 | -> Binary states |
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| 147 | -> Auto |
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| 148 | ('m' && data_optn == AMINOACID): |
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| 149 | Auto -> Dayhoff |
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| 150 | -> JTT |
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| 151 | -> mtREV24 |
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| 152 | -> BLOSUM62 |
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| 153 | -> Auto |
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| 154 | - manual.html adjusted |
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| 155 | |
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| 156 | 5.0.a6 20.12.1999 - new manual.html added |
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| 157 | |
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| 158 | 5.0.a5 07.12.1999 - output bug fixed (bestrates were written before they |
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| 159 | were computed) |
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| 160 | |
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| 161 | 5.0.a4 02.12.1999 - header file inclusion ajusted: |
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| 162 | added: #include<string.h> |
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| 163 | changed from: #include "ppuzzle.h" |
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| 164 | to: #ifdef PARALLEL |
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| 165 | # include "ppuzzle.h" |
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| 166 | #endif |
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| 167 | |
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| 168 | 5.0.a3 27.11.1999 - '-h' comandline option removed, because of problems |
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| 169 | with MPICH under LINUX |
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| 170 | - new memory leaks of 5.0.a2 closed in PP_Finalize |
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| 171 | |
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| 172 | 5.0.a2 27.11.1999 - Cleanup of the source code |
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| 173 | - Measurement of CPU time added |
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| 174 | - Parallel load statistics added (quartets, trees, time) |
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| 175 | to puzzle report. |
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| 176 | - Cleanup debug messages |
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| 177 | - Comments "[...]" are removed from usertrees now. |
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| 178 | - single quotes will only be printed arount species |
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| 179 | names if -DUSEQUOTES is set at compiletime. |
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| 180 | - tree likelihood is printed infront of a tree as a |
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| 181 | comment, [ lh=-xx.xxxxx ](...); |
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| 182 | |
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| 183 | 5.0.a1 26.11.1999 - Cleanup of the directories |
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| 184 | - Copyright changes |
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| 185 | - Version changes |
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| 186 | |
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| 187 | |
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| 188 | VERSION CHANGE |
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| 189 | ============== |
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| 190 | |
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| 191 | 4.1.a26 25.11.1999 - Makefile made universal for pauzzle and ppuzzle |
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| 192 | - lines not needed removed from puzzle.h |
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| 193 | |
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| 194 | 4.1.a25 19.11.1999 - Output file prefixes for distances, trees, and |
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| 195 | puzzlereport changed in user trees analysis case |
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| 196 | to user tree file name |
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| 197 | - Temporary output of likelihood to treefile added |
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| 198 | |
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| 199 | 4.1.a24 11.11.1999 - Output of puzzling step trees changed |
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| 200 | ptorder: [ orderno # % ID #UniqTopos #Steps ]PHYLIP |
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| 201 | pstep: chunk #InChunk sum ID #UniqTopos #Steps |
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| 202 | - preliminary leap frog RNG implemented, i.e. uses |
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| 203 | the rand4 in the usual way in the sequential case. |
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| 204 | If run in parallel all rand4 are initialized with |
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| 205 | the same seed and started with PP_Myid-th random |
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| 206 | number. after that each process uses the every |
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| 207 | PP_NumProcs-th random number to make sure that these |
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| 208 | unique. |
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| 209 | |
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| 210 | 4.1.a23 08.11.1999 - output of sequential and parallel version to *.pstep |
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| 211 | made identical |
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| 212 | |
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| 213 | 4.1.a22 05.11.1999 - two different puzzle step tree outputs intruduced |
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| 214 | and added to the menu ("[ 1. 35 ](...);": |
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| 215 | - ordered unique tree list -> *.ptorder |
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| 216 | Format: "[ 1. 35 ]" (Ordernumber, Amount) |
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| 217 | - chronological tree list -> *.pstep |
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| 218 | Format: "[ 1. 35 ]" (Chunknumber, Amount in chunk) |
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| 219 | (the last is a problem in parallel, because the come |
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| 220 | in chunks, as scheduled) |
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| 221 | - debugged the output |
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| 222 | 4.1.a21 04.11.1999 - Makefile adjustments for other Plattforms |
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| 223 | - pstep tree output changed. unique treestructures |
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| 224 | printed to *.pstep file with a leading comment |
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| 225 | containing an order number and the ammount padded |
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| 226 | with blanks (e.g. "[ 1. 356 ]('mouse'..."). |
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| 227 | output is done right before writing the puzzle file. |
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| 228 | - controlled MPI finish to the Quit menu option added |
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| 229 | |
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| 230 | 4.1.a20 03.11.1999 - some garbage collection (free) added |
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| 231 | - makefile adjusted, OFLAGS for optimization added |
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| 232 | (ppuzzle/MPICH has problems with -O, so the |
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| 233 | ppuzzle is created without optimization) |
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| 234 | Some minor changes in the makefiles |
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| 235 | - still to do: garbage collection from 'internalnode' |
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| 236 | in master process |
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| 237 | |
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| 238 | 4.1.a19 13.10.1999 - adding the output of standardized (i.e. sorted) |
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| 239 | puzzling step trees. Those are printed to the |
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| 240 | standard output at the moment. (Routines to sort |
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| 241 | and print the trees implemented) |
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| 242 | 14.10.1999 - routines for printing the sorted trees to a string. |
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| 243 | needed to send them between Master and Worker, and |
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| 244 | to have a unique key to sort and count the trees. |
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| 245 | 21.10.1999 - counting of sorted trees implemented by doubly linked |
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| 246 | list, sort routine, print to stdout |
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| 247 | 25.10.1999 - change place of writing distances to file right after |
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| 248 | distances have been computed. |
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| 249 | - output of puzzling step trees now with true name, |
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| 250 | not numbers |
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| 251 | 02.11.1999 - parallel counting and sending of puzzling step trees |
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| 252 | - some parallel sending bugs fixed |
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| 253 | |
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| 254 | 4.1.a18 14.09.1999 - adding possibility to specify input file at |
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| 255 | command line, this specifies also the output |
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| 256 | filenames (puzzle output: *.puzzle; treefile: |
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| 257 | *.tree; distances: *.dist; Triangel EPS: *.eps; |
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| 258 | unresolved: *.qlist; puzzling step trees: *.pstep) |
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| 259 | If an unexisting name is given, one has to reenter |
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| 260 | the right name, but the wrong one is used as prefix. |
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| 261 | 15.09.1999 - sending back of bad quartets from slaves added |
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| 262 | - bug in quart2num fixed (not used before; was shifted |
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| 263 | by 1) |
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| 264 | - first version of a README added ;-) |
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| 265 | |
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| 266 | 4.1.a17 03.08.1999 - Recv-Error in receiving DoPuzzleBlock fixed |
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| 267 | - double freeing of same MPI_Datatype fixed |
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| 268 | - changing of scheduling algorithm to smaller chunks |
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| 269 | in gss -> sgss |
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| 270 | 13.09.1999 - bug fixed in optimization routine in ml2.c: |
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| 271 | boundary check added |
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| 272 | |
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| 273 | 4.1.a16 12.07.1999 - slight changes in verbosity levels |
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| 274 | - changed all printf to FPRINTF(STDOUTFILE to |
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| 275 | change easily from stdout to a file. |
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| 276 | |
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| 277 | 4.1.a15 08.07.1999 - scheduler for both parallel parts |
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| 278 | - several small changes |
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| 279 | |
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| 280 | 4.1.a14 25.06.1999 - computation of tree parallel, scheduler dependent, |
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| 281 | sending all biparts in one message instead of one |
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| 282 | by one |
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| 283 | - several small changes since a13 in sched.c, et al. |
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| 284 | |
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| 285 | 4.1.a13 10.06.1999 - computation of tree parallel (chunk = #trees/#slaves) |
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| 286 | - scheduling schemes implemented for minimum chunk sizes |
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| 287 | |
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| 288 | 4.1.a12 07.06.1999 - computation of quartets properly parallel |
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| 289 | - scheduling implemented |
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| 290 | - counting of quartets by slave ajusted |
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| 291 | - TODO: sending of bad quartets (array + list) |
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| 292 | - distinction between '1st user tree' and 'NJ tree' |
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| 293 | in result output removed again |
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| 294 | |
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| 295 | 4.1.a11 28.05.1999 - PP_SendDoQuartBlock, PP_RecvDoQuartBlock, |
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| 296 | PP_SendQuartBlock, PP_RecvQuartBlock |
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| 297 | - mallocquartets() changed from global to local |
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| 298 | variables to be more flexible |
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| 299 | - Quartet computation moved to slave (badquartet |
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| 300 | handling missing: output, badquartet vector); |
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| 301 | - distinction between '1st user tree' and 'NJ tree' |
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| 302 | added in result output (puzzle1.c around l.1756) |
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| 303 | |
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| 304 | 4.1.a10 20.05.1999 - num2quart, numquarts, quart2num introduced |
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| 305 | - parallel init/finalize, quartets computed on |
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| 306 | master and slave, compared -> equal -> all necessary |
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| 307 | parameter exported |
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| 308 | |
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| 309 | 4.1.a9 19.05.1999 - 'dvector forg' removed from onepamratematrix |
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| 310 | cmdline, because it's not used in the function. |
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| 311 | |
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| 312 | 4.1.a8 18.05.1999 - add _GAMMA_ (not necessary) to gamma.h and _PUZZLE_ |
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| 313 | to puzzle.h to avoid dublicate includes, possible |
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| 314 | due to ppuzzle.h |
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| 315 | - ppuzzle added to makefile and to check |
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| 316 | - 1st parallel version but no slave computations |
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| 317 | only sending parameters and done signals. |
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| 318 | |
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| 319 | 4.1.a7 18.05.1999 - export reevaluation of tree and evaluation of |
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| 320 | usertrees to evaluatetree. |
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| 321 | |
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| 322 | 4.1.a6 17.05.1999 - -DNEWFORLOOP added to fixed.src, because the changed |
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| 323 | for loop structure changes the sequence of randomized |
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| 324 | quartets during likelihood mapping |
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| 325 | - change 'int main()' to 'int main(argc, argv)' |
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| 326 | - export more functionalities from main: |
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| 327 | memcleanup(), inputandinit(&argc, &argv) |
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| 328 | - grouping if's (excluding eachother) together in |
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| 329 | switch() |
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| 330 | - split treereavaluation and 1st usertree, |
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| 331 | evaluate all usertrees together (TODO: both, |
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| 332 | treereavaluation and usertrees in one loop) |
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| 333 | - MAKE CHECK added to ./makefile |
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| 334 | |
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| 335 | 4.1.a5 16.05.1999 - adding Ždvector BrnlengthŽ to lslength cmdline to |
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| 336 | reduce globality of Brnlength. (Later better to *Tree) |
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| 337 | |
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| 338 | 4.1.a4 11.05.1999 - structure of for loops changed in computeallquartets |
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| 339 | and recon_tree, so that the quarted addresses are in |
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| 340 | one contigous sequence (for a<b<c<d). This reduces |
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| 341 | swapping on low memory machines and is easier to |
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| 342 | parallelize. |
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| 343 | |
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| 344 | 4.1.a3 07.05.1999 - export likelihood mapping from main to map_lklhd() |
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| 345 | - export tree reconstuction from main to recon_tree() |
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| 346 | |
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| 347 | 4.1.a2 06.05.1999 - moving all quartet_(a)lklhd calls to a general |
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| 348 | purpose routine compute_quartlklhds() |
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| 349 | |
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| 350 | 4.1.a1 06.05.1999 - Macro constants for typ_optn and puzzlemode |
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| 351 | for better readability. |
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| 352 | - Ring counter for typ_optn and puzzlemode in |
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| 353 | the menu realized with mod (%) instead of IF. |
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| 354 | - Possibility added to switch to a fixed random |
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| 355 | seed (-1) or/and fixed 'random' integers (0) |
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| 356 | by using -DFIXEDRANDSEED and -DFIXEDINTRAND options. |
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| 357 | |
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| 358 | |
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