MapQTL 6 Release Notes ====================== === 13 November 2020 === Maintenance release of MapQTL 6 (Build: 13nov2020.24feb2020) A minor bug relating to phase types is repaired. === 10 November 2020 === Maintenance release of MapQTL 6 (Build: 10nov2020.24feb2020) The analysis of multiple traits in a single session could result in runtime errors or singularity errors starting from the second trait, but only for these situations: - population type BC1 with B and H genotypes - population type HAP with loci having phasetype PH1 - population type BCBxF0 which result in singularity errors under the regression algorithm or log-domain errors under the mixture model; and these situations: - population type BCBxFy with y>0 - population type CP which may result in above errors, but usually there will be contrasting results between neighbouring map areas. The results will be different from the correct results obtained when the trait is analysed separately in his own session. This bug is repaired. === 3 March 2020 === Maintenance release of MapQTL 6 (Build: 3mar2020.24feb2020) The file with the release notes can be viewed using a new option of the Help menu. The program is now so-called 'DPI aware', which means it automatically looks better on a high resolution monitor. If the scales of the Y-axes of the charts are determined automatically, then now the Y-value(s) of the horizontal lines (if to be drawn) are taken into account. In cases with singularity or perfect fit, the permutation test combined over populations could end up with the error message 'error in combined permutation test'. This is corrected. The information provided regarding singularity and perfect fit on the Session tabsheet of the permutation test is expanded. Previously, it only reported the numbers of cases with singularity and perfect fit on the entire linkage group. Now, these numbers are presented for all positions analysed on each linkage group. The genome wide analysis and the combined analysis over populations still just report these numbers for entire genome and entire linkage group singularity or perfect fit, while the details are given in the reports of the individual traits. Regarding singularity and perfect fit, it should be noted that it is highly preferable to resolve these problems prior to any final analysis. === 4 June 2013 === Maintenance release of MapQTL 6 (Build: 4jun13.4feb11) Minor internal adjustments. Improved installer. === 12 March 2013 === Maintenance release of MapQTL 6 (Build: 12mar13.4feb11) An error was detected in the reported means and additive effects under interval and MQM mapping of population type BCBxFy: - mu_A contained the results of mu_B and mu_B those of mu_A; - as a result of this, the additive effect contained minus the correct additive effect. The error is corrected. The means were reported correctly under the Kruskal-Wallis analysis. === 11 January 2011 === Maintenance release of MapQTL 6 (Build: 11jan11.9feb10) Additions: The option 'Clear All Trait Nodes' is added to the Edit-menu; it will clear the selections for analysis of all traits of all populations. A pop-up menu is added to select or de-select for analysis all (numerical) traits of a population or all commmon traits. The menu is activated by right-clicking on a population node or the Common traits node, or by pressing the space bar when a population node or the Common traits node is selected. === 17 February 2010 === Maintenance release of MapQTL 6 (Build: 17feb10.9feb10) Minor internal adjustments. === 6 May 2009 === Final release of MapQTL 6 (Build: 6may09.10mar09) Changes: In the Kruskal-Wallis analysis of population type CP under the classification type (hh,k-) the results of class k- were presented in the columns of class ll; this is corrected. The minimum number of permutations is reduced to 10 for timing purposes. The permutation test in the presence of design cofactors and/or covariates was done in a theoretically incorrect way. Now the permutation test is done on the data residuals obtained by subtracting the effects of cofactors and/or covariates (as estimated under the interval mapping null hypothesis) from the trait values. === 17 April 2009 === Pre-release of MapQTL 6 (Build: 17apr09.10mar09) Changes: The new manual is included as pdf document, available under the Help-menu. The pop-up menu for special selection of traits for analysis is improved. The workings of the "Common traits" node are improved. Navigating in the results by clicking on group nodes in the session tree now also applies to the "Results (cont'd)" tabsheet. The permutation test in a combined analysis now produces a "Genome wide" node as a child of the Combined node. The additive effect of cofactors in a BC1 was given a factor 2 too small, now it is given correctly. === 10 March 2009 === Pre-release of MapQTL 6 (Build: 10mar09.10mar09) Automatic cofactor selection for traits combined over populations is available. This is the nearly final version of the program. The rewriting of the manual is the only remaining task. === 13 February 2009 === Pre-release of MapQTL 6 (Build: 13feb09.5sep08) The permutation test for traits combined over populations is available. === 20 January 2009 === Pre-release of MapQTL 6 (Build: 20jan09.5sep08) Populations can be combined in interval mapping, MQM and restricted MQM mapping analysis. First the individual populations are analysed, subsequently the combined LOD score (or deviance) is calculated. Charts can be made showing the combined LODs as well as the LODs and other parameters of the separate analysis results. (Automatic cofactor selection and permutation test for traits combined over populations will follow later.) === 4 December 2008 === Pre-release of MapQTL 6 (Build: 4dec08.5sep08) Covariates and simple experimental design cofactors (e.g. blocking) can be used with interval mapping, (r)MQM mapping, automatic marker cofactor selection and the permutation test, now both with the Haley & Knott regression approximation and with maximum likelihood as QTL analysis algorithm. === 26 November 2008 === Pre-release of MapQTL 6 (Build: 26nov08.5sep08) The results for the covariates and design cofactors are now shown in a table. The results for the marker cofactors as used to be shown in the cofactor monitor file are added to this table, this cofactor monitor file is not used anymore. The table is in the extra tabsheet called "Results (cont'd)". The preceding two releases contain errors in analyses using covariates or design cofactors; these are corrected. === 14 November 2008 === Pre-release of MapQTL 6 (Build: 14nov08.5sep08) Covariates and simple experimental design cofactors (e.g. blocking) can be used with interval mapping, (r)MQM mapping, automatic marker cofactor selection and the permutation test, but ONLY if the Haley & Knott regression approximation is chosen as algorithm. The results for the covariates and design cofactors are not yet shown in a table (but will be later). === 11 November 2008 === Pre-release of MapQTL 6 (Build: 11nov08.5sep08) Covariates and simple experimental design cofactors (e.g. blocking) can be used with interval mapping, automatic marker cofactor selection and the permutation test, but ONLY if the Haley & Knott regression approximation is chosen as algorithm. === 16 October 2008 === Pre-release of MapQTL 6 (Build: 16oct08.5sep08) This release is not final. There are several features that still need to be added, such as use of covariates and simple experimental design cofactors. Also the manual needs to be adapted to this version and printed. Changes with respect to MapQTL 5: = The code behind the user interface was overhauled to give an even more stable program. The interface itself hasn't changed much. = The Haley & Knott regression approximation to maximum likelihood interval and MQM mapping was added. Advantages of the regression approach are a magnitude higher speed and reduced use of RAM memory, while the quality of the approximation is generally quite good. = Three population types that can be analysed were added: DH2: doubled haploid population drawn from an F2, one doubled gamete from one F2 plant BCpxFy: advanced backcross inbred line family; starting from the BC1 repeatedly backcrossing to the same parent (as used for the BC1) of each individual resulting in a single offspring per individual, followed by selfing with single seed descent; the backcross parent p and the generations x and y must be specified: p = A or B, x is the number of backcrosses including the one for creating the BC1: 1 <= x <= 99, y is the number of selfings: 0 <= y <= 99, BCa1F0 is equivalent to BC1 IMxFy: advanced intermated inbred line family; starting from the F2 repeatedly random intermating (preferably chain crossing) the individuals resulting in a single offspring per individual, followed by selfing with single seed descent; the generations x and y must be specified: x is the number of intermatings including the two for creating the F2: 2 <= x <= 99, y is the number of selfings: 0 <= y <= 99, IM2F0 is equivalent to F2, IM2Fy is equivalent to RIx with x = 2 + y MapQTL 5 Release notes ====================== === 23 July 2008 === Maintenance release of MapQTL 5 (Build: 23jul08.7apr08) = When no project is open, pressing the OK button on the Environment and the Analysis Options dialogs will save the options as default options that will apply to all future projects (similar to the 'Save as default' button). = The About box was renewed. === 9 April 2008 === Maintenance release of MapQTL 5 (Build: 9apr08.7apr08) Changes: = A few minor (internal) improvements were made. === 4 April 2008 === Maintenance release of MapQTL 5 (Build: 4apr08.11mar08) Changes: = An error was corrected in the (r)MQM calculations for the RIx population type. The error affected the outcome in situations with a high level of missing marker information, for instance when all markers on a linkage group are scored in a dominant fashion. In such cases the estimated genotype means and additive effect would be different, the LOD score and the explained variance were not very much affected. = Rounding errors could cause the LOD score in interval mapping to be negative, with extremely small values like -10^(-13). This would affect the permutation test resulting in an error message 'error in permutation_test()'. Both in interval mapping and MQM mapping such negative values are now truncated to 0.0. = Also due to rounding errors interval mapping and MQM mapping could occasionally fail to compute the results for the last marker on a linkage group. This is corrected. === 7 May 2007 === Maintenance release of MapQTL 5 (Build: 7may07.4oct06) Changes: = MapQTL 5 was enabled to run under Windows Vista. For installation under Windows Vista, please see the 'Installation ReadMe' file. === 4 October 2005 === Release of MapQTL 5 (Build: 4oct05.1jun05) Changes: = If under (Restricted) MQM Mapping no null hypothesis (H0) could be calculated on an entire linkage group (due to singularity or perfect fit) a runtime error occurred; this is corrected. === 15 March 2005 === Release of MapQTL 5 (Build: 15mar05.29dec04) Changes: = When opening a project the linkage group names for each session are read from the Session Info tabsheet, however only the first 200 characters from the appropriate line were read whereas with longer group names and many groups the line would be much longer, which resulted in error messages like 'Error reading chart options ...'. This is corrected and now the group names are printed on the Session Info tabsheet over multiple lines (if necessary) and all of them are read. === 18 August 2004 === Release of MapQTL 5 (Build: 18aug04.2feb04) Changes: = The GIC (genotypic information coefficient) for the CP population was not output completely, only for the first parent (GIC_1). This release displays all GIC values for the CP population: GIC_1, GIC_2, GIC_m. === 20 July 2004 === Release of MapQTL 5 (Build: 20jul04.2feb04) Changes: = The GIC (genotypic information coefficient) for the RIx population type was calculated as for an F2, as shown in the manual. However the GIC for an RIx should be generation dependent, which is corrected. The right GIC formula for RIx is that of the F2 in the manual where the factor 2 before the summation is replaced by 1/(2*p), with p the Mendelian expected frequency of the A genotype for the given generation x in RIx; e.g., for RI2 (= F2) p=0.25, thus the factor 1/(2*p) is 2; for the 'infinity' generation, p=0.5, thus 1/(2*p)=1. This change results in higher GIC values (for RIx only) especially in between marker positions. = The percentage progress is shown on the Windows task bar next to the program name. = MapQTL could not deal correctly with situations where the Windows regional settings did not use the point as the decimal separator. Now MapQTL is forced to use the point as the decimal separator (i.e. within MapQTL only), so that everything functions correctly if there is a different decimal separator than a point, with the exception that sorting columns of numbers with decimal parts is done as if the numbers are text (this is due to an internal problem with the used ActiveX component for the tables). === 2 March 2004 === Release of MapQTL 5 (Build: 2mar04.2feb04) Changes with respect to the pre-release: = The user manual is finished. = The Results tabsheet is filled only after the calculations (KW, IM, MQM, rMQM) are done for all linkage groups; this used to be done concurrently with the calculations which made everything rather slow. = The Calculate button hint (shown when the mouse pointer is over the button) will tell what is required to enable the button in case it is not enabled. = The chart axis titles were not drawn with the chart font indicated on the environment options; this is corrected. = The preset default mapping step size is now 1.0 cM. = The Session Info tabsheet lists the used statistic: LOD or Deviance. === 4 Feb 2004 === Pre-release of MapQTL 5 (Build: 6jan04.2feb04) This release is nearly final. Only the manual needs to be adapted to this version and printed. Changes with respect to MapQTL 4.0: = The user interface was completely revised to give you more ease of use, better QTL charts and improved exportability: - multiple populations and maps in a single project; - analyses stored in sessions for (re-)inspection; - much improved QTL charts with many options; - data in user adjustable and exportable tables; - print preview. = Computationally only the interval mapping of RIx populations was changed; a speed-up is achieved by setting an analysis option to use an approximation; the alternative is the original (slower) method; especially the permutation test of RIx benefits from the speed-up. = The genotypic information coefficient is added. = The license file system is overhauled: - when there is an evaluation or temporary license, a (paid up) license file can be installed using a Help-menu option; - license information can be viewed using a Help-menu option; - the licensed organisation is shown in the About-box. = Options (including the list of last used projects) are stored in the 'MapQTL5' directory within 'My Documents'. If this does not exist it is created.