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Fixed a crash (rather than issuing an error message) if the "multilocus" option was used for simulation without the "mscoalescent" option being on, when true trees had not been assigned to each locus.Fix problems with likelihood calculation when switching between likelihood models with site-specific rates versus equal or gamma rates, or when each observed site pattern occurs in only one partition subset.Versions can updated using either an auto-updating system (GUI version) or just returning to the download site (both versions).Once we have decided to make an official release of the GUI version, it will no longer be freely downloadable, and test versions will no longer auto-update.To do this, you must use a gen RClass statement, and use "0" for state pairs between which transitions are not allowed, and an alphabetic code (a, b, ...) otherwise.E.g., for a data set containing characters with three states (0, 1, and 2), you would do "lset genrmatrix=(a 0 b)" to indicate that transitions between states 0 and 1 occur at one rate (a), between 1 and 2 occur at a different rate (b) and transions between 0 and 2 are disallowed.This version fixes several bugs and adds a couple of enhancements; most changes involve under-the-hood work in preparation for the release of version 5.0.
Win32 font handling was also refactored to increase code-sharing between Mac and Window versions.
While final development and testing is underway, we are making these test versions available as a free download.
They will expire every few months, and you will need to update when this happens.
Fixed a problem with accessing an out-of-bounds memory location while reading trees after one or more taxa had been deleted.
Although the data read from this address were never actually used, the problem could nonetheless cause a memory violation (and crash) on some operating system versions (Windows 8 and later, and possibly some Linux systems as well). Please join the (low-traffic) Google group paup-announce to receive announcements of updates by email.