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. ------------------------------------------------------------------------ 1999 ------------------------------------------------------------------------- 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 no 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