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