What's new in GenoDive 2.0 Beta 27
Sep 17, 2014
- Hopefully (again) fixed error where opened documents were not visible.
- Interface tweaks for Mac OS X 10.10 Yosemite.
- Sidebar no longer has a gradient, and has a more modern shade of blue.
- Excluded data are now a little bit more transparent.
- Corrected tons of tooltips.
- Slightly different way of storing and accessing user preferences.
- First steps towards 64-bits support.
- Removed cruft.
New in GenoDive 2.0 Beta 26 (Sep 9, 2014)
- It is now possible to export data in Arlequin format, using the newly added Export-command in the File menu.
- Removed support for Growl notifications.
- Hopefully fixed error where opened documents were not visible.
- Fixed bug where an empty table was shown in dialog for saving multiple files.
- Fixed rounding error in calculation of p-values in hierarchical AMOVA.
- Fixed copy-paste error in output of G-statistics.
- Fixed bug in Model Matrix based on clones.
- Help files are now validated xhtml.
- Better support for full-screen mode.
New in GenoDive 2.0 Beta 25 (Oct 31, 2013)
- Drastically improved performance with large datasets by showing only a subset of the loci in the Matrix View.
- Stopped support for OS 10.4 (Tiger) and 10.5 (Leopard); GenoDive now requires 10.6 (Snow Leopard) or newer. As a side-effect, GenoDive no longer runs on computers with a PowerPC processor.
- Switched to different random number generator.
- Fixed bug in PCA that occurred with datasets with lots of invariable loci.
- Fixed bug in Spatial Autocorrelation that occurred when using the average value instead of Mantel's r.
- No longer tries to reopen previous windows on Lion and Mountain Lion.
New in GenoDive 2.0 Beta 24 (Apr 20, 2013)
- Fixed bug in the results of the permutation test of AMOVA with unbalanced sampling sizes (with previous versions the values of the F-statistics were correct, but the p-values were off).
- Population assignment can now allow for a user-specified rate of self-fertilisation.
- K-means clustering is now less restrictive in the maximum number of clusters that can be entered.
- Now correctly states in results that standard deviations of F-statistics are calculated, not standard errors.
- Improved reading of BayesAss files.
- Improved reading of Distance matrices.
New in GenoDive 2.0 Beta 23 (Oct 27, 2012)
- Added correction for missing dosage information for polyploids to multiple analyses.
- Much improved manual, made from Help-files.
- Filling of missing data can now also correct the dosage of polyploids.
- Added stratified Mantel test, removed constrained Mantel test.
- Better calculation of Smouse & Peakall distances.
- Fixed crashing bug in opening of Results.
- Fixed crashing bug in calculation of distance classes.
- Fixed bug in results of clone assignment.
- Principal Components Analysis now uses Gst instead of rho.
- Testing clonal propagation now works when replacing missing data with average allele lengths.
- K-means clustering no longer flags best clustering according to AIC.
- Now less stringent in requiring enough free memory to calculate distances.
New in GenoDive 2.0 Beta 22 (Jan 17, 2012)
- Genetic diversity now has bootstrapped confidence intervals that do not just consist of zeroes.
- Corrected eror in calculation of heterozygosity for polyploid populations of small size.
- Now automaticaly parses Results files on opening, for better compatibility with Lion.
- Added calculation of confidence intervals using bootstrapping for AMOVA and G-statistics.
- AMOVA no longer removes individuals with missing data, but fills the missing data with random alleles.
- Calculation of genetic diversity now works better for datasets with lots of missing data.
- The number of decimals in the results can now be set by the user.
- Fixed bug in special include of populations.
- Correct writing of individual names in Genetix format.
- Fixed small bug in interface of Transformation.
- Better error checking in reading of population names.
New in GenoDive 2.0 Beta 21 (Aug 8, 2011)
- Improved handling of missing data in K-means (frequency-based), PCA, spatial autocorrelation, and some distance calculations.
- Introduced multiple new methods of redefining populations in the transformation of marker data.
- Added support for data files in "Convert"-format.
- Fixed bug in calculation of some between-individual distances.
- Fixed popup menu in Import and Convert windows.
- Miscellaneous small bug fixes.
New in GenoDive 2.0 Beta 20 (Apr 4, 2011)
- Added calculation of genetic diversity.
- Added per-population testing to assignment test.
- Fixed error in Monte Carlo permutations of assignment test.
- Fixed bug in making clone corrected dataset using Special Include.
- Added Nei's Gst, Meirmans & Hedrick's G''st, and Jost's D as pairwise distances.
- GenoDive now correctly gives the p-value for negative values of Gis.
- Demoted "Matrix with Residuals" from separate analysis to a part of the Mantel test.
- Updated toolbar; turned "Analysis" item into "Recent analyses".
- Fixed bug in checkboxes to include or exclude loci.
- Fixed bug that could lead to a crash after saving results.
- Fixed crashing bug in Clonal Diversity.
- Subtly changed adaptive starting temperature in K-means' simulated annealing.
- Fixed small interface bug in Inspector tables.
- Changed all Phist into Fst for generality and consistency with the literature.
- Removed cruft.
New in GenoDive 2.0 Beta 18 (Aug 9, 2010)
- Introduced calculation of G-statistics, including Nei's Gst, Hedrick's G'st, and Jost's D.
- Changed main Help page for easier access to most important topics.
- Removed support for old style preferences (pre 2.0b13).
- Fixed bug in Hybrid Index that occurred when a population only had missing data at a locus.
- Miscellaneous small bug fixes.
New in GenoDive 2.0 Beta 17 (Jan 13, 2010)
- Changed clone assignment, added more info to the histogram and fixed a crashing bug.
- Fixed bug where the program would sometimes not quit.
New in GenoDive 2.0 Beta 16 (Nov 18, 2009)
- Improved compatibility with Mac OS 10.6 "Snow Leopard".
- Removed possibility to show splash screen at startup, as this could lead to crashes.
- Fixed bug in reading of GenePop format.
- Internal restructuring of assignment procedures.
New in GenoDive 2.0 Beta 15.1 (Oct 30, 2009)
- Fixed bug in Geographical distances introduced in 2.0b15.
New in GenoDive 2.0 Beta 13 (Jan 6, 2009)
- Major speed increase in K-means clustering using simulated annealing; made it possible to repeat the algorithm a certain number of times.
- Changed interface for K-means clustering to make better use of speedier simulated annealing.
- Fixed bug in K-means clustering using hill-climbing, is now slightly slower as a result.
- Expanded the options in the transformation of marker data.
- Added calculation of pairwise Phi'_st (Phi_st standardised relative to the within population diversity).
- Added calculation of pairwise Rho, an Fst-analogue that is independent of ploidy and double reduction.
- Fixed bug in pairwise Phi_st calculation with unbalanced population sizes.
- Fixed bug in Population Assignment, where excluded populations were sometimes taken into account.
- Changed output of Population Assignment, now the likelihood of the current population is also displayed.
- New bundle identifier for preferences-file that matches my new homepage http://www.patrickmeirmans.com.
New in GenoDive 2.0 Beta 12 (Nov 25, 2008)
- Implemented Shuffle Data: permutation of data using randomisations or bootstraps.
- K-means clustering now also shows Akaike Information Criterion, which can also be calculated for a single cluster (k=1).
- Pairwise Phi_st-values can now correctly be calculated for haploid data.
- Fixed bug in output of clone assignment.
- Miscellaneous small bug fixes.