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: 4 major version [addition of forces, big rearrangements] 2 subversion [new options, or large bug fixes] 1 fix minor problems [fixing errors, wording etc] ------------------------------------------------------------------------- 2016 ------------------------------------------------------------------------- January 20 Migrate 4.2.6 improving numerical stability with many loci there are still issues (if you receive very different averages and modes, rerun the program with more steps, if the problem persists let me know (with infile and parmfile) ------------------------------------------------------------------------- 2015 ------------------------------------------------------------------------- October Migrate 4.2.4-5 improving stability August 10 Migrate 4.2.3 addition of hyper-prior for prior gamma distribution checking and revising code for divergence June 18 Migrate 4.2.2a and Migrate 3.6.11 missing -1 leading to a crash in printing population names found (thanks cipres-team) and fixed. June 13 Migrate 4.2.1a fixing a problem with assignment probabilities where individuals to assign are not present for all loci. May 24 Migrate 3.6.10 memory overrun resolved when data file numpop# and relabel numpop# do not match. May 2 Migrate 3.6.9 the threaded versions crashed with msat data and fragment length translation because of an early access to the threadsafe random number generator which did not have the locks allocated: fixed. March 30 Release of Migrate 4.2.0a, addition of a recover option, that allows 'checkpointing' once the first run using bayes-allfile failed, using the recover option [see in saved parmfile] one can continue and potentially finish the run. March 26 Migrate 3.6.8 Fixed stupid typo in last update that lead to not calculating the allele frequency tables. March 23 Release of Migrate 4.1.4a, fixed an error in the divergence calculation; changed the snp allele reporting so that it can work with large number of linked snps per locus. Fixed the snp issue in 3.6.7, too. February 22 Release of Migrate 4.1.3a, added an option to do terse PDF output for very large number of loci, changed the example directory (see README in there). During January I also updated the legacy/old version to 3.6.6. ------------------------------------------------------------------------- 2014 ------------------------------------------------------------------------- December 2 Release of Migrate 4.x, current version 4.1.0a, all updates are now done in this version, although I will do bugfixes in 3.6.5 for a while to accomodate users. October 18 Migrate 3.6.5 fixes a problem with the mean over many loci. When the program was not collecting enough samples then occasionally the error could lead to incorrect histograms. If you run 3.6.4 upgrade to 3.6.5. ------------------------------------------------------------------------- 2013 ------------------------------------------------------------------------- December 15 Migrate 3.6.4/4.0 reevaluated the combination of loci in the Bayesian inference and found a bug that affects marginal likelihoods that are evident with small differences between models, this seems to be an issue with comparison based on sequence data (e.g. the Bayes factor tutorial). This problem was introduced with the correction of the marginal likelihood in 3.6. Setpember 29 Migrate 3.6.3 Added the hapmap datatype to the datatype menu. September 19 Migrate 3.6.2 Fix a problem with a potential infinite loop in the parameter proposal step that stopped some snp runs, fixed a reporting glitch with random-subset. August 24 Migrate 3.6.1 Random-subset failed on windows, now fixed August 20 Migrate 3.6 Problem with combining loci found and fixed, the correction for the overuse of the prior failed when the posterior is concentrated and sampling is sparse, leading to an overcorrection that in turn led to spurious peaks that became important with more and more loci. June 10 Migrate 4.0a Assignment on a per allele basis works, Haplotyping also works. June 6 Migrate 3.5.4 problem with UTF file type checking is causing problems on some machines, UTF checking is disabled for now, make sure that your data file does not contain any other characters than ASCII. April 28 Migrate 3.5.3 incorrect printing of random subset list in pdf file is fixed. April 15 Migrate 3.5.2 a bug in the parallel code the lead to a 1 Byte memory overrun is fixed. March 11 Migrate 3.5.1 'fixed' the skyline plots, now the plots should look OK again. Some minor formatting issues in the options. 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 give 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 intermediate 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] ------------------------------------------------------------------------- ======= 2010 ------------------------------------------------------------------------- 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. ------------------------------------------------------------------------- >>>>>>> .r1596 2009 ------------------------------------------------------------------------- <<<<<<< .mine October 30 Migrate 3.1 stable version -- some minor errors fixed ======= October 30 Migrate 3.1 stable version -- some minor errors fixed. Improvement and correction of the marginal likelihood calculations. >>>>>>> .r1596 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 ..... 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: 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=) 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 -------- $Id: HISTORY 2170 2013-09-19 12:08:27Z beerli $