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
- ./align 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<string.h>
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<b<c<d). This reduces
swapping on low memory machines and is easier to
parallelize.
4.1.a3 07.05.1999 - export likelihood mapping from main to map_lklhd()
- export tree reconstuction from main to recon_tree()
4.1.a2 06.05.1999 - moving all quartet_(a)lklhd calls to a general
purpose routine compute_quartlklhds()
4.1.a1 06.05.1999 - Macro constants for typ_optn and puzzlemode
for better readability.
- Ring counter for typ_optn and puzzlemode in
the menu realized with mod (%) instead of IF.
- Possibility added to switch to a fixed random
seed (-1) or/and fixed 'random' integers (0)
by using -DFIXEDRANDSEED and -DFIXEDINTRAND options.