./biology/puzzle, Maximum likelihood analysis of molecular sequence data

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Branch: CURRENT, Version: 5.2, Package name: puzzle-5.2, Maintainer: babafou

PUZZLE is a computer program to reconstruct phylogenetic trees
from molecular sequence data by maximum likelihood. It implements
a fast tree search algorithm, quartet puzzling, that allows
analysis of large data sets and automatically assigns estimations
of support to each internal branch. PUZZLE also computes pairwise
maximum likelihood distances as well as branch lengths for user
specified trees. Branch lengths can also be calculated under the
clock-assumption. In addition, PUZZLE offers a novel method,
likelihood mapping, to investigate the support of a hypothesized
internal branch without computing an overall tree and to
visualize the phylogenetic content of a sequence alignment.
PUZZLE also conducts a number of statistical tests on the data
set (chi-square test for homogeneity of base composition,
likelihood ratio to test the clock hypothesis, Kishino-Hasegaw a
test). The models of substitution provided by PUZZLE are TN, HKY,
F84, SH for nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62 for
amino acids, and F81 for two-state data. Rate heterogeneity is
modelled by a discrete Gamma distribution and by allowing
invariable sites. The corresponding parameters can be inferred
from the data set.

Required to run:

Required to build:

Master sites:

Filesize: 854.631 KB

Version history: (Expand)

CVS history: (Expand)

   2021-10-26 12:03:45 by Nia Alarie | Files touched by this commit (73)
Log message:
biology: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes
   2021-10-07 15:19:44 by Nia Alarie | Files touched by this commit (73)
Log message:
biology: Remove SHA1 hashes for distfiles
   2019-11-02 23:09:01 by Roland Illig | Files touched by this commit (10)
Log message:
biology: align variable assignments

pkglint -Wall -F --only aligned --only indent -r
   2015-11-02 19:42:23 by Alistair G. Crooks | Files touched by this commit (38)
Log message:
Add SHA512 digests for distfiles for biology category.

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.
   2013-04-01 10:56:43 by Steven Drake | Files touched by this commit (1)
Log message:
Mark as not MAKE_JOBS safe.
   2012-09-11 22:32:15 by Aleksej Saushev | Files touched by this commit (31)
Log message:
"user-destdir" is default these days
   2010-09-19 10:38:14 by OBATA Akio | Files touched by this commit (3) | Package updated
Log message:
Update puzzle to 5.2.
Based on PR#43775 by Kamel Derouiche.

5.2       14.07.2004    - Version 5.2 !!!


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


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
			- writeOTU_orig, writetree_orig, resetedgeinfo_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

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

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 !!!
   2009-09-15 00:12:56 by Zafer Aydogan | Files touched by this commit (1) | Package updated
Log message:
update master_sites. remove ftp.ebi.ac.uk. file has been removed.