H I S T O R Y    O F      M I G R A T E 


[people] in brackets helped with resources or reported problems.


Version numbers: 3 major version [addition of forces, big rearrangements] 
                 3 subversion                   [addition of new options]
		 0 fix minor problems        [fixing errors, wording etc]  

-------------------------------------------------------------------------
                                     2013
-------------------------------------------------------------------------
March 11      Migrate 3.5.1 'fixed' the skyline plots, now the plots
              should look OK again.
March 3       Migrate 3.5 added a Gamma distributed prior, added the 
              prior distribution to the histogram in the PDF, to show how
              different the posterior is from time prior. Changes in the 
              calculation of Nm (in contrast to M [m/mu]) that should 
              fewer problems than the earlier implementation. Running with
              'no data' now works for all cases.
January 26    Migrate 3.4.6 Fixed a reporting bug that did increase the
              printed accepted and tried samples when in a parallel run
              the number of nodes was smaller than replicates*loci. 
January 4     Migrate 3.4.5 compilation on windows using cygwin works now.
January 2     Migrate 3.4.4 fixes a problem for maximum likelihood
              introduced in 3.3.1, the autotune feature introduced a memory
              overrun with likelihood, but not with Bayesian inference.
              Changed printout presenting relative mutation rate from data.
-------------------------------------------------------------------------
                                     2012
-------------------------------------------------------------------------
December 17   Migrate 3.4.3 fixes a crash when the burn-in is zero.
December 11   Migrate 3.4.2 Electrophoretic marker data was not read correctly
              due to a programming error (the program crashed), now fixed 
              [thanks to Chester Sands for reporting]
December 6    Migrate 3.4.1 A report suggested that on some cluster computers
              the generation or random number seeds leads to a stall because
              the queried device does not deliver enough randomness and
              therefore blocks, since we do not need cryptographically usable
              random numbers the reader was changed to the non-blocking
              random device, this does not affect windows machine because
              those use the system clock (inferior).
November 24   Migrate 3.4 added a few commandline options (-version, -help)
              the -version command is used to test the fastmigrate-n 
              installation for macintosh distribution 
November 10   Migrate 3.3.5 when using Nm instead of M and also using a
              restricted custom migration matrix sometimes warnings were
              triggered, the problem was found and fixed (values for 
              undefined parameters were recorded bu not used).
October 25    Migrate 3.3.4 Under some condition a problem with the combination
              of loci lead to empty posterior distribution diagrams and 
              huge negative numbers for the marginal likelihood. My underflow
              protection failed on, well, for some runs. This fix still needs
              more review but looks good so far. I skip the version 3.3.3 
              because I had an internal one that was released on some binary 
              distributions. Some reporting during the run has changed.  
August 26     Migrate 3.3.2 Fixed a memory problem that made it problematic to 
              run datasets with many populations (and parameters).[Romain Mayor]
August 22     Migrate 3.3.1 Change of data distribution system for parallel
              version, this allows to faster start with many (>500) loci.
	      Inclusion of autotuning for Metropolis-Hastings acceptance ratio
              this has promoted a change in the defaults for the proposal:
              now it is back to Metropolis-Hastings instead of Slice sampling.
Jul 22        Migrate 3.3.0 Bayes factor subsystem revised and improved.
              Version bump because of changes in menu ordering. 
June 13       Migrate 3.2.21 does fix a bug that lead to problems when you 
              analyze reduced custom migration matrices using parallel 
              version and also did not save the bayesallfile [this should 
              fix the infamous empty posterior histogram problem]]
May 20        Migrate 3.2.20 revision of the inheritance scalar system.
              the earlier versions did not work well.
May 10        Migrate 3.2.19 allowes now #M and #@M in the data file to
              estimate microsatellite repeat lengths from fragment lengts. 
-------------------------------------------------------------------------
                                     2011
-------------------------------------------------------------------------
October 8      Migrate 3.2.17 fixed a problem when all parameters are set
               to average (m) and no interdiate file for Bayesian inference
               is used. Fixed a problem for windows that caused a crash when
               intermediate files for Bayes inference (bayesallfile) was
               used. 
July 1         Migrate 3.2.16 removed some printing in the MPI version and 
               fix of a condition that lead to print ? instead of numbers
               for the allele frequency tables (msats and iam datasets)
June 10        Migrate 3.2.15 found a mistake that was incorporated on
               May 30 that resulted in incorrect sampling of genealogies
               when the option fast-likelihood=NO and DNA data was used.
               The output then showed near zero acceptances for genealogies
               and extremely low ESS for the genealogies. This is fixed.
June 8         Migrate 3.2.14 reissue of the last update because I pushed
               older version onto the website, to avoid confusion the correct
               version is labeled 3.2.14.
May 30         Migrate 3.2.13 Fixed two memory problem that lead to 
               occasional crashes in the likelihood inference module.
               Addition of testsuite that allows testing and comparing
               speed of different compilations and settings.
May 26         Migrate 3.2.12 Fixed warnings for Ubuntu Linux.
May 19         Migrate 3.2.11 I have started to use a testsuite to check 
               more regularly on small glitches: the testsuite directory 
               contains datafiles, a python script to run automated tests,
               the parameter warning system had a glitch with ML and 
               parallel runs, now fixed.  
May 14         Migrate 3.2.10 fixing and underflow problem with snp data 
               when the number of individuals are large, this particularly
               affected model choice runs because the hottest chain often
               failed because snps did not use scaling of the conditional
               likelihood values on the genealogy; the fix introduces such 
               a scaler with the same option that is used with the sequence 
               data.
May 1          Migrate 3.2.9 Streamlining code
March 21       Migrate 3.2.8 Cleaning of little nuisances detected by the 
               static analyzer in xcode, investigation of strange posterior
               with parallel runs and custom migration matrices and replicates.
               Revised the "Warning" section, to "Suggestions". 
January 12     Migrate 3.2.7 Parallel Migrate had difficulties with Maximum
               likelihood printing of profiles tables (it crashed),
               temporary fix (the exchange of data among computer nodes 
               needs to be more streamlined (time frame depends on funding)).
-------------------------------------------------------------------------
                                     2010
-------------------------------------------------------------------------
December 5     Migrate 3.2.6 Parallel Migrate broke for Bayesian inference
               when the reporting file bayesallfile was set to NO: fixed.
November 27    Migrate 3.2.5 a memory overflow in reporting large migration
               matrices in the ML-mode is fixed [Daniel T. R.]
November 21    Migrate 3.2.4 cleaning up of printing and using inheritance 
               scalars. First trial distribution of a general fastmigrate
               python script.
November 5     Migrate 3.2.3 the PDF library was not able recognize the shipped
               zlib.h, hopefully fixed now.
October 31     Migrate 3.2.2 clean up problems with zlib in the configure file.
               No change in functions in the program.
October 25     Migrate 3.2.1 addition of a compression scheme for the recording
               of all parameter values in the Bayesian inference (simple add
               a .gz to the filename of the bayesallfile filename and it will be
               compressed, the source distribution now distributes also the zlib
               library and configure can be forced to use that, default is the
               system, but that may be slow. Little tests with very large datasets
               have been done for the compression scheme. Printing of trees 
               now also works for microsatellite trees. Currently the printing of 
               ALL trees using the parallele migrate does not work (use the single
               cpu version).
October 5      Migrate 3.2 addition of new microsatellite reading method
               with an additional inputline in the infile, Migrate can now
               use fragmentlength as input. Even decimal values (as delivered
               by the .... machine as raw data can be used when the additional
               input lines specifies the repeat lengths, ambiguous alleles will be 
	       assigned to repeats using a simple probability model that assigns to
               to the lower repeat number with a triangular probability distribution, crossing 0.5
               when the actual fragmentlength is exacly in the middle of two repeat alleles.
               Addition of a system to report problematic configuration or runtime issues, this is
               work in progress and may need some user feedback. Currently problems with upper bounds
               of prior specifications and too low Effective sample sizes are reported.   
September 15   Migrate 3.1.10 fix of a glitch with replicates and marginal
               likelihoods and replication (replication was not divided out)
               [thanks to Anders].
September 8    Migrate 3.1.9 reestablish the reading of old bayesallfile to
               recreate the output of an older run, I am still working on the 
               tool to combine several old bayesallfiles so that users can run
               loci indpendently on different machines and then later get a 
               combined estimate [thanks to Chris Drummond for helping to squash
               several of the key problems]
August 9       Migrate 3.1.8 memory fixes so that very large datasets
               (>100 populations) have a chance to run [whether these converge
               I do not know].
July ~15       Migrate 3.1.7 Cosmetic changes so that my Bayes factor tutorial
               and the migrate menu match.
May 24         Migrate 3.1.6 turned heating back on that got turned off to 
               find a problem in 3.1.4. [Yuma More]
May 14         Migrate 3.1.5 Fixed problem in combining multiple loci when the
               Bayesian inference was using exponential prior distributions.
April 30       Migrate 3.1.4 problem with not allowing very very low migration
               rates anymore fixed [my fix on March 21 was obviously to 
               brush.
March 21       Migrate 3.1.3 fixed two issues that affected microsatellite
               data (migration rates had tendency to be close to zero,
               population sizes overcompensated for that, this problem was
               introduced with 3.0.8/3.1).
February 6     Migrate 3.1.2 after way too many ours of porting the new
               migrate version to windows (relearning what I thought was 
               standard on decent platforms). Many little changes to 
               accomodate windows. 
January 15     Migrate 3.1.1 fix a bug that prevented to show results for
               the first migration rate.
January 1      Migrate 4.0alpha allows for haplotypic data using mixed
               data types (sequence, msat, snps, ... ) all with different
               mutation models. Free combination of completely linked and
               and unlinked segments. Migrate allows the use of
               libhmsbeagle to calculate likelihoods on trees using the
               GPU and other speedups [not all options are allowed yet
               because beagle is not supporting all options.
-------------------------------------------------------------------------
                                     2009
-------------------------------------------------------------------------
October 30     Migrate 3.1 stable version -- some minor errors fixed. 
               Improvement and correction of the marginal likelihood 
               calculations.
August 1       Migrate 3.0.8 problems with tree printing and dated samples
               reported (thanks to Trevor Bedford) hopefully fixed. 
May 24         Migrate 3.0.7 Population relabeling possible, but only 
               using the parmfile,
               several small problems with relabeling may still persist.
May 5          Migrate 3.0.6 Memory issue with MPI printing resolved, 
               Slice sampler speed-up results in about 25% faster runs 
               (for small runs). 
January 8      Migrate 3.0.5 Dated samples with multiple loci should work now
-------------------------------------------------------------------------
                                     2008
-------------------------------------------------------------------------
December 8     Migrate 3.0.4 reporting of ESS and autocorrelation in MPI parallel runs
               fixed, this problem does not appear in single or thread runs and does not affect 
               accuracy in the MPI runs.
December 3     Migrate 3.0.3 Bayes factors tested and seems to work fine, first exploration of 
               approximation of Thermodynamic integration using only 4 chains to approximate true
               integral (using Bezier curve that approximates curve from 32 chains).
October 22     Migrate 3.0.2 Added a configure option (at compile time) so that one can
               force the PDF outputfiles to be letter size (default) or A4 size.
October 20     Migrate 3.0.1 Fixed bugs in the ML calculation on parallel computers with 
               replication (thanks Jeff Row).  
August 1       Migrate 3.0 updated manual, cleaned some small things, included skyline plots,
               and migration events, dated samples. 
July 10        Migrate 2.5.2 Internal rearrangements for preparation of 
               skyline plot calculations. Change Makefile so that all particular
               Apple platforms work.
June 10        Migrate 2.5.1 
May 13         Migrate 2.5 Changes of the configure/make files so that the
               compile choices highlight only the most important compile 
               targets. The compile on AIX systems should work now, although some
               tweaking is still needed.
April          Migrate 2.4.4 Fix of a random number seed problem in the windows
               distribution, some earlier version delivered always the same 
               automatic random number seed.
February 19    Migrate 2.4.3 The Bayesian inference printed wrong values when
               the prior was excessively large compared to the posterior,
               if your posteriors cover only a small fraction of the prior
               range you need to rerun (an indicator of the problem is the
               large discrepancy of the mean and mode. This problem does not 
               affect likelihoods.
January 22     Migrate 2.4.2 The parallel code was executing the likelihood 
               ratio test multiple times, on some systems this caused a crash,
               fixed.
January 9      Migrate 2.4.1 A problem with reading options for genealogy
               summaries fixed. Missing file in source code added.
January 5      Migrate 2.4 Several improvements moved into the mainstream
               program: marginal likelihood calculations, histogram of 
               migration events over time and probability of location of
               most recent common ancestor, standard Mac(Intel) distribution
               contains now a parallel cluster utility using all avaialable
               CPU cores. 
-------------------------------------------------------------------------
                                     2007
-------------------------------------------------------------------------
December 16    Migrate 2.3.4 Fix of a memory problem that made long 
               runs with some data impossible.
               Memory management changed considerably for genealogies. 
August 26      Migrate 2.3.3 Reordering of output (the MCMC run characteristics
               appear now all at the end.
August 14      Migrate 2.3.2 An error that affected runs using heating with 
               the stepwise mutation model is fixed.
July 20        Migrate 2.3.1 Problem with SNP model solved (thanks to Ivo 
               Chelo reporting the problem).
July 12        Change of default threshold value for stepwise 
               microsatellite mutation model
June 26        Migrate 2.3 Improvement of the speed of the stepwise model 
               by a huge factor (reorganizing code).
January 1      Migrate 2.2.0 Improvement of memory consumption of parallel
               runs, some cleaning up of wording in output, addition of slice
               sampling proposal mechanism, revision of manual to reflect the
               program better. Fix of a problem in Brownian motion datatype
               introduced late November in 2.1.9 (only in prerelease version).
               Relative mutation rate estimation from data.  
-------------------------------------------------------------------------
                                     2006
-------------------------------------------------------------------------
October 21     Migrate-2.1.9 Several minor problems with heating and 
               custom-migration matrix under Bayesian inference are fixed.
September 8    Migrate-2.1.9 Problem with switching between ML and Bayes analysis fixed,
               without this fix a simple switch between methods without adjusting priors
               resulted in priors that did never change (resulting in an obviously 
               wrong result).
August 8       Migrate-2.1.8 Several smaller fixes and improvements
               fix for wrongly reporting acceptance of swaps between heated chains
               when using a Bayesian framework, several minor errors: when user mix 
               infile and parmfile in the commandline option a warning is issued, when 
               the data looks like an xml file the data import is aborted.[skyline plots are
               still experimental!!!!!].
June 8         Migrate 2.1.7 reducing memory footprint for bayesian analysis
               rearrangments in the migration history code. Changed histogram module
               now can plot histograms for events (was mig-histogram) and skyline plots
               similar to the ones by Strimmer and Pybus (2001)[rigorous tests are still not done]
April 27       Migrate 2.1.6 buf fix in the profile table writer for PDF, that
               crashed with some datasets and some machines (Macs, Others?)
April 11       Migrate 2.1.5 working on improvement of the PDF output file, MCMC-ML table 
               and profile tables, and percentiles tables should work now.
March 6        Migrate 2.1.4 several cleanups and streamlining of the functions
               related to microsatellites to gain speed, addition of an option to override 
               the menu option in the parmfile (migrate-n -nomenu parmfile or
               migrate-n -nomenu parmfile). 
February 2     Migrate 2.1.3 Bug that resulted in crashes in windows binary found and fixed
January 14     Migrate 2.1.2 Memory problem with multiple replicates in ML method
               fixed, migration-histogram problem fixed, both probably introduced on 2.1.0
-------------------------------------------------------------------------
                                     2005
-------------------------------------------------------------------------
December 24    Migrate 2.1.1 Use of valgrind to clean up some memory problems,
               memory footprint should be somewhat reduced
December 4     Migrate 2.1.0 Bayesian inference overhauled and rechecked,
               changes in interface in parmfile interface (use write in the
               menu to bring your parmfile up to date). Addition of a PDF
               printing interface, the Bayesian analysis is mostly complete
               in PDF, the maximum likelihood PDF interface is still lacking
               major parts. The ASCII output file is still the safest resource 
               for ML. Several minor changes to menu and option printing.
July 20        Migrate 2.0.7 Sumfile naming option fixed, MPI version 
               does not stall anymore when number of nodes and loci match.
               Profile tables code cleaned.
May 14         Miggui 0.8 release of Macos 10.3+ graphical user interface
               programmed by Carl McIntosh.
May 13         Migrate 2.0.6 Cleaning up of Bayesian menu options, 
               Bayesian method with multilocus-microsatellite data
               still needs more tests, if you get failures please report them.
               Several minor memory leaks and one major leak in the Bayes code
               fixed.  
January 24     Migrate 2.0.5 A string buffer read error in sgets() and 
               a memory leak [Kelly Gallagher, Karl Schmid] in the tree 
               changing algorithm fixed. Some compilation issues on 
               windows machines fixed, should work now with MS Dev Studio. 
-------------------------------------------------------------------------
                                     2004
-------------------------------------------------------------------------
December 27    Migrate 2.0.4 Fixed Parmfile-reader that missed the usertree option, 
               menu was not affected by this problem.
November 29    Migrate 2.0.3 prior distribution and menu/options revised,
               Migrate documentation revised and Bayesian Inference added, plotting problem with
               multiple population solved.
October 14     Migrate 2.0.2  error in option reader (LRT, theta, and Migration rates) 
               found and fixed
September 17   Migrate 2.0.1 parallel runs failed on some machine entering profile calculation
               memory problem found and fixed.
July 27        Migrate 2.0 (alpha) Test release for the Molecular Evolution workshop
               at MBL in Woods Hole, MA. Introduction of Bayesian search strategy, 
               introduction of distribution of replication scheme 
               among multiple computers. The parallel version now distributes loci and 
               replicates over a cluster using the standard message passing interface.             
July 26        Migrate 1.8.2 Bayesian version nears completion, Bayesian-version
               runs using MPI in multiple replicates and at the end summarizes 
               over the loci-histogram, program bayeshist put into the contributed 
               folder. Bug with recording all trees while using heating fixed [Daniel Myers]
May 21         Migrate 1.8.1 addition of replication to the parallel scheme
               now it is possible to run replicates in parallel, if there are
               enough free compute-nodes.
May 1          Migrate 1.8 changes to the parmfile writing and reading parts
               a parmfile contains now the complete syntax of all available
               options in commentlines. Fix of a memory problem when the custom
               migration matrix and the number of populations are not in sync.

-------------------------------------------------------------------------
                                     2003
-------------------------------------------------------------------------
December 13    Migrate 1.7.7 under some conditions the parallel version crashed while
               reading the sequence data into the tree
October 23     Migrate 1.7.6 with very large numbers of loci the program crashed during reading
               the data file, for some datasets this fix did not work, and because I
               had this version up for a short while on the ftp site I increase the version
               number.
October 14     Migrate 1.7.5 with very large numbers of loci the program crashed during reading
               the data file.
August 04      Migrate 1.7.4 fix accidently deleted line for ADAPTIVE heating.
June  15       Migrate 1.7.3 MPI works now on IBM regatta (SP4) machines.
February 24    Migrate 1.7.2 working on problems with heating and gamma-deviated
               mutation rates.
February 2     Migrate 1.7.1 more checking, removal of a typo bug that 
               shortens long chains (introduced in restructuring process in 1.7). 
January 27     Migrate 1.7 added option so that one can choose whether the
               missing data gets discarded or not for the allelic data types
January 3      Migrate 1.7 Revised printout for likelihood ratio test [bug 
               testing help Peter Pearman], inclusion of AIC (Akaike's 
               information criterion). Inconsistency for custom migration
               matrices filled with '0' and 'm' fixed [Peter Pearman].
               updated list of papers that cite migrate. Migrate compiles 
               in parallel using MPICH (I still prefer LAM (www.lam-mpi.org)). 
               Addition of Makefile specification for IBM SP3. 
               (711 registrations)
-------------------------------------------------------------------------
                                     2002
-------------------------------------------------------------------------
November 29    Migrate 1.6.9 If you run microsatellite data and used 
               versions 1.6.7 or 1.6.8 you need to rerun because there was 
               a data reading problem in that version
               and this is fixed now [I am sorry about this].
August 12      Migrate 1.6.8 problem with reading weighfiles and
               catfile solved [Jon Seger]. Change of printing
               routines in the parallel version, all workers
	       send now to the master who is the print-center.
July 12        Migrate 1.6.7 fixed problem with large sumfiles [Alex Wang].
June 25        Migrate 1.6.6 fixed a reporting problem with adaptive heating.
	       Second and hopefully final fix of of "?" for *all* allele data 
	       types [Eric Simandle]  
June 16        Migrate 1.6.5 nasty bug in microsatellite and allele code fixed:
               when "?" were present then the second replicate could end up 
               with the incorrect number of tips in the genealogy and the 
               program would fail. [Alex Wang, Deirdre Joy], a related problem
               that occured when only 1 individual was scored for 1 
               msat allele in a population is fixed, too [Russell Pfau]. 
               Memory overrun with brownian mutation model and heating fixed.
June 05        Migrate 1.6.4 Problem with SNP data reading fixed, currently
               running simulations to see if SNP works. 
May 23         Migrate 1.6.3 Some more minor problems in the parallel 
               implementation fixed.
May 20         Migrate 1.6.2 Problem with msat data distribution in the
               parallel version fixed [Eric Simandle]
May 13         Migrate 1.6.1 Fixed a fatal bug in the profiles when using
               profile=All:FAST [Martin Damus].
April 13       Migrate 1.6 In the infile the number of individuals per locus with 
               sequence data  can now be different, to accomodate different numbers
               of individuals change the population line to
               <num ind locus1> <num ind Loc2> ..... <num ind loc m> Population name
               the old syntax will still work and still assume that in a population all loci
               have the same number of sequences.  
April 12       Migrate 1.5.1 Fixed a problem when using sumfiles and replicates
               the profiles had difficulties to find the maximum.
March 28       Migrate 1.5 change of maximization routine, jumps far away
               from the driving values are penalized using a normal distribution
               with mean=param_0 and std=param_0, this should help that 
               with some data sets the program will refrain to jump to
               ridiculously high values, although if your data suggest such values
               the program will go there, just more slowly. Addition of adaptive
               heating (MCMCMC) to help to search the solution space better.
February 18    Migrate-1.4 Problems with custom migration matrix fixed
               but profile tables with symmetric 4Nm have problems (@#$^&%@),
               symmetric M works.
-------------------------------------------------------------------------
                                     2001
-------------------------------------------------------------------------
December 18    Migrate-1.3.3 two buffer over-runs in the parallel part
               found and fixed, this affected Linux machines but not MacOSX
December 2     Migrate-1.3.2 Profile tables work again for settings 
               profile=YES:FIXED and profile=YES:QUICK, I obviously broke 
               these settings in version 1.2.4 [Martin Damus, Mats Bjorklund]
November 12    Migrate-1.3.1 In parallel version: the data file is only read 
               by the master node and the distributed to the worker nodes.
October 28     Migrate-n 1.3 (minor bug fixes related to plotting and parallel 
               MPI execution)  changes so that profiles are now calculated 
               parallelized over parameters instead of loci. This will 
               reduce network traffic and should finish much faster if there 
               are as many cpu as there are parameters. Improvement in the
               the ML calculation [replaced the line search with a newer version]
August 15      Migrate-n 1.2.4 fix for geographic distance file option, some older 
               versions [most likely version that were newer than 1.1] were using
               a similarity matrix instead of a distance matrix.
August 9       Migrate-n 1.2.3 On Compaq alpha the program crashed with
               underflows (EXP(-1000)=NaN and not 0 as everywhere else),
               now every EXP() will be safeguarded on Compaq alphas.
August 8       Migrate 1.2.2 Several minor fixes to "beautify" outfile and
               menu printing.
July 28        Migrate-n 1.2.1 changes to the menu to incorporate AIC for
               migration model selection, needs documentation.
July 15        Migrate-n 1.2 Reworking of microsat likelihood calculation.
               It seems that my change on April 15 was only doing half
               of the job, the conditional likelihood calculation
               were not taking into account unobserved alleles above and
               below the smallest and largest repeatnumber.
               Everybody using microsatellite data should upgrade. 
April 30       Migrate-n 1.1 Reworking of likelihood calculation,
               should speed up parameter estimation about 10-20%.
               Inconsistency between manual likelihood-ratio description
               and program fixed, manual is now at version 1.1.
               If you want to use likelihood ratio test you should
               run 'long' runs or then use replication or heating.        
April 20       Migrate-n 1.0.4 Harmonizing the use of end-of-line
               characters,  migrate had several problems 
               reading files that were moved between different
               operating systems, hope this is all fixed now. 
               Fix of FAST and QUICK profile options [Raphaelle Chaix].  
April 18       Migrate-N 1.0.3. More fixes, plots should work now 
               [Steven Irvin], windows binary now is compiled with 
               correct set of C-files and not old ones [Mats Bjoerklund].
April 15       Migrate-N 1.0.2 Serious problem in microsatellite code
               found and fixed: the stepwise-mutation model was only 
               approximated due to a programming error. The probability 
               of the number if steps for a given length of time was only
               too crudely approximated. Without the error reports of
               Steven Irvin and Raphaelle Chaix I would not have found 
               this. Problem with "?" as the last character in a file
               transported between different operating systems fixed 
               [R. Chaix]. Error in new replicate-summarizing code fixed
               [S. Irvin].
April 11       Migrate-N 1.0.1 Glitch in single locus likelihood ratio test
               fixed (technically you should not use this anyway).
               Some small formatting issues when saving parmfile.
April 10       MIGRATE-N 1.0 several memory leaks fixed, plotting
               option changed and will plot only over all loci.
               Many internal changes/speedups that should not affect users,
               although may introduce no bugs. Gamma deviated mutation rate
               among loci changed considerably but still has difficulties
               to converge. Sumfile run with "allelic" data broke,    
               fixed now.
February 12    MIGRATE-N 0.9.14 some cleanup on freeing memory in profile
               evaluation. Fixed a bug in the heating code when the dataset
               is "allelic data" [Robb Brumfield].
------------------------------------------------------------------------
                                     2000
-------------------------------------------------------------------------
December 16    MIGRATE-N 0.9.13 Speed up: memcpy() in site rate category code
               is replaced by pointer swapping [C++ newsgroup contribution],
               more precalculation of parts of the acceptance-ratio 
               calculation. Can use now a geographical distance file to 
               specify a kind of an isolation by distance model. 
               Rearrangement of likelihood ratio test menu [Steven Irvine], 
               removal of the l-ratio=LOCUS option, l-ratio=MEAN is replace 
               by l-ratio=MLE, this actually should not break old parmfiles. 
December 05    MIGRATE-N 0.9.12 Bug fix: I broke the infinite allele code
               and it is fixed now again [Ron Goldthwaite]
November 26    MIGRATE-N 0.9.11 Bug fix: when compiled optimized on SUNs
               the program showed odd and wrong behavior, and did not
               accept any new genealogy after a while, perhaps it is
               a compiler problem, because it does not occur on Linux
               Intel and I have not found a memory problem. A more
               restrictive array copying seems to remedy the problem.
               Additions: Adapted for compiles in a MAC OS X terminal
               window, it runs about twice as fast as in MAC OS 9.
               Addition of an option for more accurate calculations 
               during the data likelihood calculations with large data
               sets where the individual probabilities underflow and the
               program crashes, this option is not necessary for many 
               data sets, but slows the down run around 20-40%.   
October 18     MIGRATE-N 0.9.10 Bug fix: Multiple microsatellite loci analyzed
               with Brownian motion model, populations with no data, and a
               missing value in at least one of the sampled populations 
               crashed, because the whole locus was discarded, it should 
               work properly now [Martin Damus] 
October 13     MIGRATE-N 0.9.9 Bug fix: Parallele evaluation on symmetric 
               multiprocessor machines now works with rate categories (more 
               than one process wrote to the same unguarded memory).
               Further redesign to easy transition to parallele processing 
               of loci. 
October 6      MIGRATE-N 0.9.8 Bug fix: The reanalysis of a sumfile
               with one locus failed in the profile likelihood calculation.
               Addition of saveguards for machines (Dec Alphas) 
               that return for EXP(-1000) = NaN instead of a very small 
               number or zero. 
               Addition of a sequencing error 
               possibility [see under Datatype with Sequence data]. 
               Heating scheme expanded from 4 chains to n<20 chains.
July 28        MIGRATE-N 0.9.7 Bug fix: in cases where a population size
               cannot be well estimated (the likelihood surface is flat)
               the reset function failed to calculate an average size, 
               and returned 0.0 which resulted in erratic behavior
               [Patricia Brito].
July 22        MIGRATE-N 0.9.6 Addition of a logfile option, 
               the Gamma-deviated mutation rate among loci seems to work
               but needs more rigorous testing, so sometimes it will still
               fail. 
July 11        MIGRATE-N 0.9.5 Bug fixes: the addition of a null population
               should work now for all datatypes [Martin Damus], 
               under some conditions the maximizer
               gave up too quickly, and (an embarassing one) for profile 
               likelihood percentiles miscalculation of percentile values: 
               some of the  old percentiles were wrong, To see what impact it
               had on your conclusions see below 
               correct/:1%   5%   10% 25%   50% 75%   90% 95%   99%
               wrong/old:  0.5% 2.5%  5% 12.5% 50% 87.5% 95% 97.5% 99.5%
               The old tables were using the 1,5,10... labels but calculated
               values under "wrong/old".
               [the likelihood ratio tests are not affected by this]
               The new profile tables are set so that you can generate
               99%, 95%, 90%, 50% confidence intervals. 
               [mutation=Gamma is still broken, sigh]  
May 30         MIGRATE-N 0.9.4
               Fixed a bug in reading and writing summary files
               (options affected were write-summary and datatype=genealogy).
               mutation=Gamma is still broken [Eric Simandle], 
               do not use it.
May 12         MIGRATE-N 0.9.3
               embarrased to say but the last fixed introduced a problem,
               in the likelihood calculation, hopefully  fixed now.
               mutation=Gamma is still broken [Eric Simandle], 
               do not use it.
April 22       MIGRATE-N 0.9.2
               inconsistency in likelihood calculation with replication
               fixed.
April 21       MIGRATE-N 0.9.1
               Bug in Mac-version of automatic random number seed
               generation, and in recording start migration parameters fixed,
               and migration start parameter mix up in parmfile 
               fixed [all Ken Wahrheit]. 
               Heating scheme changed, implemented a 4 parallel chain
               heating scheme (simulated tempering) based on Geyer and
               Thompson. The Tempered transition method (Neal) will 
               be reimplemented in a later version.
               Fixes: ttratio now works for different values 
               [Judite Alves],
               Registered users: 423 
                                 (tried to find this time all doubles)
March 3        MIGRATE-N 0.9
               First introduction of estimation of parameters 
               over multiple chains or multiple runs. 
               Problems: Multiple chain/runs 
               with the combination of gamma deviated mutation rate 
               does not work yet. Heating scheme is broken.
------------------------------------------------------------------------
                                     1999
-------------------------------------------------------------------------
December 10    MIGRATE-N 0.8.5
               Change of defaults: plot=FALSE, moved eventloop()
               in plot routine for Macintosh.
December 2     MIGRATE-N 0.8.4
               Revision of likelihood ratio test output. Change
               of "burn-in" default from 200 to 10000.
               Minor speedups in several functions.
November 23    MIGRATE-N 0.8.3
               Revision of heating scheme. But still needs more testing.
November 5     MIGRATE-N 0.8.2
               Addition of a convergence criterium: Gelman's R,
               (use progress=verbose)
               Added material to the 
               likelihood ratio test documentation.  
               Several minor bugfixes (sumfile related [Tonya Bitner],
               Profile Quantile table, verbose Progress reporting)
               Registered users: 372 
September 7    MIGRATE-N 0.8.1
               More cleanup of C-code, incorporation of new spline
               routine ( but this is still experimental). Improvement
               of documentation.
August 20      MIGRATE-N 0.8
               A problem with the UPGMA starting tree fixed,
               with many individuals the starting tree contained 
               some silly ordering, that produced uneven number of
               migration events on this tree and needs rather a long
               time to recover from this.
               profile likelihood speed improvements when there is a
               custom-migration matrix with zeroes.
               Registered users: 322
June 4         MIGRATE-N 0.7.1
               Division by 0 bug fixed in fst-calculation, this seems
               to bother only DEC Alphas.
June 1         MIGRATE-N 0.7
               Updated documentation, several minor things, warnings and error
               reporting should be more consistent, I am adding a section to
               the manual that describes all error/warning messages [partly
               done], the plotting graphics are more flexible now, but still
               need more work. You can specify the range and type of 
               axes (log-scale, std-scale), and if the migration parameter
               shall be plotted as M=m/mu or 4Nm. Fix of inconsistency 
               in migration value menu input [Reinaldo Brito]. 
               Fix of an error in the
               profile-method=FAST (it will need now more time to finish,
               because it is doing the final maximization over all other
               parameters), if you want its old behavior, that assumes that 
               Theta and M are not correlated [not a too bad assumption], 
               then use profile=YES:QUICK.  
March 8        MIGRATE-N 0.6.3
               Updated documentation (fixed errors in description of
               random-seed options, added important material 
               to profile-likelihood) , 
               inclusion of improved man page,
               fixed configure for SGI's with out gcc. 
Feb 14         MIGRATE-N 0.6.2 
               Tree traversal debug code removed,
               this killed runs with many individuals [Lisle Gibbs]
               Configure for SGI changed, does it work?
               MIGRATE-0.4: no change.
               Registered users: 280.
------------------------------------------------------------------------
                                     1998
-------------------------------------------------------------------------
December 29    MIGRATE-N 0.6.1 Multilocus estimates are all wrong 
               in version 0.6, silly programming mistake found an fixed.
               If you have used microsatellites or electrophoretic markers
               or several sequence loci you need to rerun that analysis.
               Result table should print now nicer with population numbers 
               above 3.  
               MIGRATE-0.4: no change.
               Registered users: 234
Oct 29         MIGRATE-N 0.6
               Addition of datatype=n that is for single nucleotide
               polymorphism data, no simulation with this kind of data
               is yet done, so I do not know about biases etc. 
               Profile tables now report 4Nm instead of m/mu for
               the migration parameters.
               Documentation changed and contains now more about 
               how to read the outfile and what you can and 
               cannot do with the reported log(likelihood) values 
               [Mats Bjorklund].
               Binaries for OPENSTEP available [thanks to Magnus Nordborg
               giving me an account on his machine].
               Registered users: 206
Sep 1          MIGRATE-N 0.4/0.5 [was not released, was too busy with 
               other things]
               FST start values work now also for microsatellite data
               but I still need to check  the correctedness of the FST table
               when the data are microsatellites.
               Fixed wrong emmigration plots. Fixed wrong start 
               calculations for allelic data when a delimiter was used,
               and several minor bug fixes. Profile-method
               "uncorrelated" from version alpha.1 recovered.
               Registered users: 197
June 14        MIGRATE-N alpha.3 and MIGRATE-0.4.2
               Several minor changes in migrate-n: menu addition for
               -profile method: 
               profile-method=<Spline | Percentiles | Discrete>
               Spline: uses 1-dimensional splines to find percentiles,
               faster than the "Percentiles" option but not so accurate,
               "Discrete" evaluates at "fixed" (0.02, 0.1, 0.2, 0.5, 1, 2,
               5, 10, 50) * MLE of parameter.
               -with progress=yes you can see now a rough prognosed time 
               of end of sampling genealogies and if you use profiles 
               an estimated time of finishing.
               -Fix of reading in intermediate results (sumfile).
               -Most importantly a (hopefully) stable compile for 
               Windows, I failed to find the cause why the program
               compiled with WATCOM failed to finish with "bigger" data sets,
               it is now compiled with mingw32/gcc-win32, this is
               a windows port of the same system I am using on my workstation.
               Please report failures, I can only try a limited set of 
               examples.
               Migrate-0.4.2: new windows binary (using mingw32/gcc-win32)
               Registered users: 163
May 30         MIGRATE-N alpha.2 and MIGRATE-0.4.1
               With more than 2 sequence loci, there was a problem
               with the T/T-ratio, when the ratio was not specified 
               for each locus.
               Start parameter problems with microsatellite data fixed
               [Mats Bjorklund]. 
               Persistent problems with Windows executable
               sometimes I get floating point errors, on all other systems
               this does not occur.
               Registered users: 153
May 29         MIGRATE-N alpha.1 and MIGRATE-0.4
               Memory bug in FST calculation found and fixed
               [Daniel Yeh] 
               No change of Migrate-0.4
               Registered users: 148.
May 26         MIGRATE-N and MIGRATE-0.4
               This release has the two population version (Migrate-0.4) 
               and an alpha-version of Migrate-n that can solve migration
               matrix population model with unequal population sizes and
               unequal migration rates for n populations, I tried up to 10
               and the results where fine, but I am pretty sure that if 
               you try to feed in all your date of 100 subpopulation it
               will (a) probably crash, but more importantly (b) will
               need TERRIBLY long to run. 
               I would like to get some 
               feedback about what you want to see in the outfile,
               menu etc. Registered Users: ~138.
February 25    MIGRATE 0.4 (was not put up onto the website, I was to busy)
               More complex sequence evolution models (categories,
               weights, autocorrelation etc.) should work now, 
               it was broken. Cleanup of some output file lines, and
               some menu entries. The FST estimation (Remember FST is only 
               used to generate start parameter values) is 
               in pre 0.4 versions logically flawed. It estimates 
               2 parameters per population using F_within and F_between,
               but there is only 1 F_between. Correctly, we can
               only estimate maximally 3 parameters with 1 locus for
               two populations. I added an option into the MENU and into
               the PARMFILE (fst-type=<Theta | Migration >) with which you 
               can decide which parameter is considered the same for both
               populations.
               Registered users:89
------------------------------------------------------------------------
                                     1997
------------------------------------------------------------------------
August 20      MIGRATE 0.3.1
               Confusing menu entries for start theta and 4Nm values
               fixed [Carol Reeb], the start migration values are now
               4Nm and *not* m/mu values as before. Automatic Random
               number seed on Macs and perhaps on other Systems 
               delivered sometimes negative values, now fixed 
               [Carol Reeb], although I would recommend to use your
               own random number seeds: best values are 4n + 1 in the 
               range of 5 .. 2147483647, so there are plenty of 
               start random number seeds. Menu entry for
               usertree options should be now more clear, the usertree
               options needs a genealogy with migration events on
               it [Tony Metcalf]. Currently MIGRATE can construct 
               those, or you have to do it by hand, if you need to do 
               this send me email, because the doc is not updated. 
               Registered users:52
June 20        MIGRATE 0.3.0. 
               Brownian motion approximation to stepwise mutation
               model for microsatellites added.  Solved problems:
               Input problems with microsatellites data, major memory
               allocation problem for datasets with more than 100
               gene copies fixed [Carol Reeb].  Update of some
               citation  and FST output tables [Byron Adams].
               Persistent problems: Long sequences AND high number of
               individuals need nuch longer chains than the proposed
               default. Try ten times longer "long" chains. Or use
               the option "moving-steps".  
               Registered users:38
May 12         MIGRATE 0.2.1a. 
               Fixed problems: Interleaved sequence data
               should work now, last character of individual names is
               now printing, and printing of second population data
               should work, too, although the EP data printout is
               still ugly.  [Allen Rodrigo]. Memory problem with some
               Allelic data fixed.  
               Registered users: 30
April 30       MIGRATE 0.2a released.
               Fixed problems or changes:  Corrections of several
               minor problems, Printing of the data fixed, but still
               ugly; Memory problem with large sequences fixed.
               Options: treefile added, can write now a genealogy
               with migrations; the option progress=Verbose for more
               information during a run, the progress=Yes gives now
               less information than before. Output: covariance
               matrix for combined loci now prints, too.  Persistent
               problems:  -Long sequences need very long chains to
               remove the starting conditions for the migration rate
               from the first tree (see documentation).
               -Microsatellites still have probably a bias downwards
               in Theta, but I need more simulations to make this
               more clear.  
               Registered users: 8
March 4        First trial release of MIGRATE 0.1a
               This release is not announced widely, because I have
               to test, almost everything including all HTMLs,
               registration, and the program itself: simulations need
               time.  Registered users: 1




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$Id: HISTORY 2140 2013-03-11 15:23:13Z beerli $


