MapDisto change log

Current version: v.

Compatibility: Excel 2019/365 (32-bit and 64-bit). Should run fine with previous Excel versions (2007 - 2016). Windows 7 and 10. To handle very big datasets (e.g., GBS and high-density array genotyping), you will need the 64-bit versions of both Excel AND Windows.

Known issues:
- Commands associated with the 'Compute RF & LOD' box of the R/qtl interface aren't available in this version. However, they are advantageously replaced by the MapDisto Addons Java module accessible from the 'Data' window

*** Changes in this update ***
- New 'import data as binary' code (not used yet)
- 'Filter loci' in 'Data' now correctly implements hard filtering
- Added a 'Keep codes' option for data filtering. This avoids transforming big data into integers
- Fixed a bug in data filtering that caused traits to be lost when data is big
- Function for creating normalized and centered-normalized data now creates traits in the range of values of the original trait
- New function to draw trait distributions from the Trait stats window

Data simulation:
- Fixed a bug that caused the map size to be 0 when simulating multiple sub-populations

QTL search:
- Added button to open Phenotype-Genotype window
- Faster trait distribution drawing in Phenotype-Genotype window (F2 NYI)
- Fixed a bug in Compare methods

*** Changes in v. ***
- Added a function to split a meta-population into sub-populations
- New 'import data as binary' code (not used yet)

Data simulation:
- Use the Framework map in the Simulation module
- Add random traits to Data
- Add simulated traits to Data now available for F2 populations

QTL search:
- Corrected a bug that caused a few markers at the end of the last linkage group to be forgotten when plotting QTLs

*** Changes in v.***

QTL search:
- Show a QTL region in Gbrowse
- QTL methods now use different output sheets
- New function to compare QTL methods (parametric, nonparametric, meta-QTL)
- 'Plot QTL' now works if only one linkage group was calculated
- 'Plot QTL' can now use physical positions if available (in marker names of type 'Chr1_xxxxxx', where 'xxxxxx' is the physical position on chromosome 1 in base pairs)
- 'Plot QTL' of metaQTL now displays individual populations together with the meta-QTL analysis

Data simulation:
- Added a function to add quantitative traits to a simulated population
- 'Use these data' now includes number of populations
- 'Export data' and 'Import data' now include Comments, Title and Cross information
- Marker names are now composed of chromosome number and physical position
- Fake population and genotype names are now created
- Trait simulation now works for F2 and SSD populations

- New function to recode genotypic data

- MapDisto no longer needs to be installed under user account. That is, it can be run from a network drive or external volume
- Old legacy toolbar is removed at startup, so it will no longer appear in the Add-ins section of Excel's Ribbon
- Browser updated for QTL results, allowing better comparison between QTL methods
- Several minor bug fixes

*** Changes in v.***

Local recombination:
- Find local recombination peaks and distribution

Data import/export:
- Read data now accepts any data codes when data is big. In the previous version it would only accept the legacy Mapmaker/EXP ABCDH- format
- Import and Export data now handle genotype names
- 'Import converted data' in the 'Addons' section of the Data window now imports the names of individuals. vbCrLf replaced by vbLf

QTL search:
- Parametric QTL analysis (ANOVA1) for all traits now displays the -Log(p) value of the F-test
- New function to find QTL peaks from QTL output
- metaQTL: One can now specify the number of populations in the Data window
- metaQTL: metaQTL analysis can now be performed on all traits at once in F2 populations
- metaQTL: Improved trait data transformation method (meta-population only)
- metaQTL: New procedure to compute stats on traits (meta-population only)
- metaQTL: Calculation of number of d.o.f in metaQTL analysis now discards pops with very low size

- QTL button names updated
- Browser updated with meta-QTL navigation

Bug fixes:
- Corrected wrong display of test name when QTL analysis performed on all traits in F2 populations
- Corrected a bug in Export data as mapmaker file. The heterozygote symbol was wrongly exported in the header

*** Changes in v. ***
QTL search:
- metaQTL: metaQTL analysis can now be performed on all traits at once (F2 populations not yet implemented). Includes QTL plotting
- metaQTL: added a function in 'Data' to transform phenotypic data for multiple populations. Allowed transformations are (1) centered and (2) centered-normalized
- metaQTL: Corrected a rare bug occurring when a F-test was equal to 0 in metaQTL analysis (except F2s)
- QTL: Added an option to draw map and trait histograms in R/qtl interface

- Added a link to online help (Google groups) in the 'About' and 'Help' sections
- Added 'Online help' button in the Splash and Main menu windows, which links to the MapDisto Google discussion group page

*** Changes in v. 2.1.3 ***
QTL search:
- metaQTL: metaQTL analysis now uses Fisher’s method to combine p-values, which is more powerful and accurate than to Sum(F) and Sum(-log10p); F2s not yet implemented
- metaQTL: Faster final step of meta-QTL analysis (except for F2s)
- metaQTL: new procedure to create centered or centered-normalized data (meta-population only)

Bug fixes:
- 'Store data' and 'Use these data' now correctly store all genotype names when Big data is activated
- 'Store data' and 'Use these data' now correctly store traits when Big data is activated
- 'Show stored data' now works as expected after running 'Use these data' from a stored dataset
- 'Draw a linkage group' can no longer use the 'Draw uniloci only' option when 'Alternate style' checkbox is unchecked

*** Changes in v. 2.1.2 ***
QTL search:
- Extended meta-QTL analysis to backcross, RIL-SSD and doubled haploid populations
- Plot QTLs now available for meta-QTL analysis
- Corrected a bug in QTL and meta-QTL analysis for F2 populations (k2 was incorrectly calculated, leading to a slightly underestimated p-value)

*** Changes in v. 2.1.1 ***
QTL search:
- meta-QTL analysis now works for the "All linkage groups" option

Bug fix:
- "Draw QTLs" from the meta-QTL window now works

*** Changes in v. 2.1.0 ***
This update concerns the R/qtl interface. The following functions are now activated:
- 'Export genotype data to R/qtl'
- 'Impute data in R/qtl' (uses R/qtl argmax procedure to impute and correct data)
- 'Import imputed data'

*** Changes in 2.0 beta versions: ***

*** Changes in v. 2.0.112 ***
Bug fixes:
- MapDisto now sets Excel to automatic calculation by default on startup
- Minor display bug fixed in the About window (arrangement of the shapes and text boxes)

*** Changes in v. 2.0.111 ***
Bug fixes:
- In "Color genotypes", corrected a bug in recombination fraction calculation for the last interval of a linkage group when the "Singleton-free RFs" box is checked

*** Changes in v. 2.0.110 ***
- Updated R version to 3.5.x

QTL search:
- New Meta-QTL analysis command for DH, BC1 and SSD and F2 populations
- Implemented Kruskal-Wallis distribution-free test for QTL detection in F2 populations

Bug fixes:
- Corrected several bugs in Phenotype vs genotype module: handling of outliers is now correct for DH, BC1 and SSD populations (Centiles, bilateral only)

*** Changes in v. 2.0.109 ***
Physical maps:
- Convert physical position (contained in marker names) to pseudo-cM in Framework map

Local recombination:
- Calculate local recombination rates from CompMap window (from the main menu, go to "Compare maps..."

Data filtering:
- Added 'Keep MD' (= keep missing data) as an option for the 'Filter redundant loci' command in "Data"
— New algorithm for filtering overpassing missing data
- Updated formulas in Filter Loci to handle 1,000,000 markers (was 10,000)

VCF handling:
- New addons now can import gzip-compressed vcf (.vcf.gz) files

- All ordering methods now do a better cleanup of previous results

*** Changes in recent previous beta versions ***
QTL analysis:
- Search QTL using R/qtl via graphical interface. Exportation of data for R/qtl. Several available methods (em, ehk, hk, mr, mr-imp, mr-argmax) and models (np, 2part). Scan types scanone and scantwo are permitted. Multiple traits scan allowed
- When simulating a population, a simulated phenotypic trait can be added

Map construction:
- Genotype imputation: Breakpoint imputation with BP-Impute (via R) by Chris Fragoso
- For F2 populations, 'Detailed map', 'Draw map', Write map' commands now handle dominant markers (although dominant markers in repulsion are still an issue and this case should be avoided for now). Useful to map dominant, monogenic phenotypic traits on a map of codominant markers.
- Export LOD/RF matrix now available for F2 populations in the 'Find linkage groups' command

- Find groups (using MapDisto Addons command) is now multi-threaded (Thanks to Chris Heffelfinger for optimizing the code)
- Faster 'Find linkage groups' (using MapDisto native command)

- MapDisto now tries to estimate computing time for long operations
- Small interface improvements
- Improved R/qtl interface
- Improved Addons interface

- Automatic installation of MapDisto Java plugins (LB-Impute, MapDistoAddons)
- Automatic installation of R/qtl
- Better handling of big datasets
- Better memory usage
- New handling of folders and subfolders: MapDisto now creates the 'MapDisto_data' and 'MapDisto_results' subfolders and places its work files there
- Several bug fixes
- Several interface improvements

- Added compatibility with Excel 2007
- Corrected a bug in map/data exportation for QGene v. 4
- Updated R/qtl interface for compatibility with R 3.4.x
- Extended calculation of recombination frequencies for RIL/SSD in case of heterozygous data to 'Draw map' command
- Added a check for Public/Private use (applies to Yale plugins)
- Added a warning message when a genotype code is encoded as ‘0’
- Improved splash screen display
- Fixed a bug in Draw map when ‘Draw uniloci only’ option is checked
- New 'Alternate style' to draw genetic maps
- Better handling of R version
- Several miscellaneous improvements
- Fixed a Mac-Windows bug that affected export of maps and data
- Bug fixes and faster computation of LOD scores for IRIL populations
- Bug fix for MapDisto_workspace folder creation when running in international versions of Excel
- More genotypes filters
- Preview filters
- Choose CRAN server for R/qtl install
- Bug fixes (in 'Read data')
- R/qtl 'Search QTL' implemented
- Compute stats on genotypes
- Filter genotypes in 'Data' and in 'Export for R/qtl' based on genotypes stats
- Compute stats on loci
- Filter loci in 'Data' based on loci stats
- Cross name in 'Data'
- File names: output file names prefixed by cross name (not yet applied to all functions)
- Soft filtering of loci
- Step option in 'R/qtl' search QTL function
- Add simulated traits to existing data
- Bug fix in marker filtering in 'Search linkage groups' (Thanks Jack Martin)
- Bug fix in 'Soft filter' option of the 'Filter redundant loci' command
- Bug fix in 'Drap map/ draw uniloci only'

Changes in older versions 2.0 beta
2.0 beta 2.0 beta 1 to 26

* Feature: compute RF & LOD in R/qtl can now find linkage groups
* Option to avoid writing RF & LOD matrix on disk in compute RF & LOD in R/qtl
* “Detailed map”, “Draw map”, Write map” commands now handle dominant markers (although dominant markers in repulsion are still an issue and this case should be avoided for now). Useful to map dominant, monogenic phenotypic traits on a map of codominant markers. [I still need to extend that to all procedures, like “Find groups”, “Matrix group”, etc…)
* changed p to -log10(p) in Khi2group procedure.
* Feature: R/qtl basic interface (Mac only for now)

2.0 beta 28
New features
* Feature: New “Convert VCF to data” feature in the ‘Data’ window
This is allowed by a new Java module by Chris Heffelfinger (S. Dellaporta’s lab, Yale University), that allows to import VCF files from Genotyping-by-Sequencing experiments into MapDisto from the ‘Data’ window. The Java program prepares a Mapmaker/EXP .raw compatible file that can be imported back in MapDisto unsung the ‘Import…’ command in the ‘Data’ window.
Note: The MapDisto.jar .vcf file has to be in the running copy of MapDisto.
Note: You will need to install the Java JKD installed (In a near future use of the standard Java RTE will eliminate this)
* Feature: New “Export data to R/qtl” feature in the ‘Data’ window.
Note: Don’t forget to choose the .csv file type before saving the file.
* Feature: New “Prepare imputation in /qtl” feature in the ‘Data’ window (uses the argmax R/qtl command).
This prepares a .Rmd file that can be run from within RStudio
Note: You will need to install RStudio, R and the R/qtl package.
* Feature: New “Drop locus summary” feature in Drop locus window.
* Feature: New “Create summary” feature in Framework map window.
* Feature: New fast Copy/Paste/Paste Transposed buttons in the MapDisto Toolbar. Useful for manipulating large matrices – the Excel 2011 built-in Copy/Paste gets very slow for large data tables.

* Improvement: Handles more than loci 32,768 (changed all Integer variable types to Long).
* Improvement: Much faster “Remove locus” command in the Main window.

Bug fixes
* bug: “Bad population type” message while importing MMK file fixed.
* bug: “Detailed map”, “Write Map”, “Drop locus” now better clear previous results
* bug: More than 5,000 loci are now allowed in Color Genotypes

2.0 beta 29
* Bug fixes

2.0 beta 30
* Bug fixes
* Reorganized code in more meaningful modules

2.0 beta 31
* Feature: New “Impute inR/qtl” feature in the ‘Data’ window.
Note: You will need to install R (use the appropriate version for your system), and the R/qtl package.
* Feature: New “Import Imputed data” feature in the ‘Data’ window.
* Some minor code changes

2.0 beta 32
* Feature: import RF & LOD matrix from MapDistoAddons.jar (ojo con los archivos pesados)

2.0 beta 33
* Feature: compute RF & LOD in R/qtl

2.0 beta 43
* Bug fix in ‘QTL/ANOVA1’: cM were not calculated properly
* ‘QTL/ANOVA1’ is now 2x faster
* ‘Extract LGs names’ from locus names is now up to 100x faster
* Handling of much bigger data - successfully tested with 87k SNPs x 322 individuals (F2 not yet implemented)
* ‘Filter redundant loci’ is now available for big data (F2 not yet implemented)
* ‘Color genotypes’ now handles more than 5,000 markers
* ‘Use these data’ from Color Genotypes now puts missing data in individuals that are not marked by a “x” or “X”
* New way to check for updates, more reliable and faster

2.0 beta 45
* Handling of much bigger data - successfully tested with 87k SNPs x 322 individuals (F2 not yet implemented)
* Drawing linkage groups now have an option to draw uniloci only. That is, if several loci are completely linked, only the first one will be displayed on the map. This allows clearer maps and faster drawing
* A new option to export maps as PDF file
* All procedures (except export routines) now use integer-type data for faster execution
* Bug fix in "QTL/ANOVA1": cM were not calculated properly
* "QTL/ANOVA1" is now 2x faster
* "Extract LGs names" from locus names is now up to 100x faster
* "Filter redundant loci" is now available for big data (F2 not yet implemented)
* "Color genotypes" now handles more than 5,000 markers
* "Use these data" from Color Genotypes now puts missing data in individuals that are not marked by a "x" or "X"
* New way to check for updates, more reliable and faster

2.0 beta 46
* New About design which now adapts to screen resolution
* QTL plots can now be exported as PDF file

2.0 beta 47
* A problem in compilation associated with message boxes fixed
* Bug fix in Find linkage groups (compute squared matrix routine)
* Dataint now declared as Byte for better RAM use_

2.0 beta 48
* Bug fix in Draw linkage groups where inter-marker distances where incorrectly reported when selecting the "Draw uniloci only"
* Export as a file now available for QTL plots when all traits are drawn at once
* Check for new versions at startup

2.0 beta 49
* New Kruskal-Wallis test for QTL analysis. This allows nonparametric or distribution free testing.
* Plot QTL now displays -log(p value) for both F-test and K&W test
* text outputs of QTL analysis now displays -log(p value) pseudo-graphs with threshold = 3

2.0 beta 50
* Minor interface changes
* LOD score for QTL analysis now derived from R-squared statistic
* Plot QTL now can display -log(p value), LOD score or F-test; LOD score is default

2.0 beta 51
* Bug fixes in Place locus and Place loci commands

2.0 beta 54
* Draw map produces more beautiful maps
* Changed the way stars for segregation distorted loci are displayed (now used -log10 of p-value)
* A few cosmetic improvements and bug fixes
* Windows version available (some Addons and R/qtl commands unfinished)

2.0 beta 57
* All Addons and LB-Impute commands now available in the Windows version (Warning: some commands have issues with Java 8, and need Java 7; affected functions are Find groups and Impute)

Previous versions
1.8.1.x (XL 2011 only)
The major new feature is an improved implementation of the Error detection method.
* Corrected a bug in Use simulated data that previously copied too many rows
* Simulations: corrected genotypic frequencies in case of segregation distortion (BC1)
Added gametic selection (F2)
Modified count formula for number of loci in each LG (XL 2011 only)

* Singleton treatment for F2s (XL 2011 only)
* p(F-test) now computed without copy/paste
* NOVA now reads loci numbers in Array instead of sheet (XL 2011 only)
* Added function of XL2004 version to plot phen vs gen in F2s (sheet just after the ANOVA1F2 sheet)
Sub: Plot_Phenotypic_Values_Vs_Genotype()
* Added a navigation menu to the "QTL" menu in the Toolbar.
* Fixed bug in copy/replace sequence from ripple (or from check inversions) that limited number of loci to copy to 250
* Compute squared matrices: Integer treatment for F2s
* Some slight optimization for BC1 (Excel 2007, 2010 & 2011)
* Big datasets: Changed several matrix formats resulting in much lower RAM consumption.
* Much faster 2-point computation

v. (Excel 2011 only)
* Spread some DoEvents in the code

v. (Excel 2011 only)
* Modified the 'Used these data' and 'Load data' commands (changed "Copy/paste" that was causing very long waitings to "load-data-in-array-then-write-in-sheet")

v. (Nov 1, 2011)
* Corrected a small bug in all versions that forced drawing of all LGs after running the Draw mapmaker map command.

v. 1.7.5 (Oct 31, 2011)
* MapDisto goes to version 1.7.5 final for Excel 2003, 2007 (Windows), Excel 2004 and 2011 (Mac OS X).
* New version for Excel 2010, which is virtually the same as for Excel 2007 except for some small changes in drawing maps.

v. 1.7 (October 25, 2007) - changes since v. 1.6:

* Feature: Compute stats in Color genotypes provides basic statistics on the allelic content of each genotype.
* Feature: "Data fit sequences" command will remove all the loci that are not present in the declared sequences from the Data window. Moreover, the loci will be re-numbered from 1 to l, if there are l loci declared. Also, the loci will be re-ordered in the Data window according to the order their appear in the declared sequences.
* Feature: Two new algorithms for marker ordering were implemented:
    * the Unidirectional Growth (Tan and Fu, Genetics 173: 2383–2390 - August 2006)
    * an improved version of the Branch & Bound algorithm, that seems to outperform the Unidirectional Growth and the seriation algorithms. (The seriation method was the first one implemented in MapDisto.) This new algorithm was tested on both simulated and real data and is very promising.
* Feature: A powerful method to improve the marker order found with one of the three algorithms available, called "Check inversions". The command will repeat the inversion procedure on all linkage group until their order is stable.
* Feature: An automatic implementation of the Ripple command, called "AutoRipple", to easily run the Ripple command on all linkage groups. The command will repeat the Ripple command until it finds the best order.
* Feature: A procedure to iteratively correct the data errors (inspired by the SMOOTH algorithm, van OS et al, Theoretical and Applied Genetics 112:187-194 - 2005). This procedure is still under testing and it should not be used for publication purpose.
* Feature: A "Three point" command, that allows to check the LOD scores for all the three-point orders of a given sequence.
* Feature: A command to remove the loci that are not assigned to a sequence. This command will also re-order the loci within the data file according to their location in the sequences.
* Feature: Color genotypes, to easily visualize and/or replace/remove the double recombinations, the candidate erroneous data points and the missing data.
* Feature: In "Options", one can uncheck the "Ripple is progressive" checkbox to get an output more similar to that of Mapmaker/EXP.
* Feature: Added the COUNT criteria for the Seriation algorithm (van OS et al, Theoretical and Applied Genetics 112:30-40 - 2005).
* Feature: Added a modified version of the CorrSum criteria for the Seriation algorithm (inspired by the criteria used in the Macintosh version of Mapmaker).
    The CorrSum is (1 - r) (1 - EXP(-LOD)), where LOD is a normalized LOD score.
    LOD = LODscore * (N / n), where n is the number of informative meioses for the pair of loci considered, and N is the total number of individuals in the population.
* Feature: A tool to graphically compare two linkage maps. The maps to be compared can easily be imported from the Main menu, Framework map, Extracted map and Simulations windows. One can also import a map from a text file, provided that it is in the standard MapDisto format.
* Feature: A new recombination fraction estimate for SSD populations, based on the paper of Martin and Hospital (Genetics 173:451-459 - May 2006)
* Feature: New simulation tool.
* Feature: Option to export map and data for QTL Cartographer (not WinQTLCart, which is already available as an option).
* Feature: Maps and populations (BC1s and F2s) simulation tool.

* Improvement: The Color genotypes command is a two times faster (but still slow).
* Improvement: Better display of QTLs when using the Draw QTLs command. The legend in Draw QTLs is now clickable for fast display of the QTLs for a particular trait.
* Improvement: Some minor interface improvements.
* Improvement: In Color genotypes, the Load data command now works independently from the Framework map.
* Improvement: Importing .out Mapmaker/EXP files now works with error detection set to on or off.
* Improvement: improved the way of computing the probability of error candidates for BC1, DH, SSD and HRILx populations. F2 populations still not supported.
* Improvement: In Color genotypes, changed "Count double recombinants" to "Count error candidates".
* Improvement: Changed the way to manage error threshold in the Iterative error detection procedure and in all the Color genotype-related commands: the new threshold is now equal to (1 - old threshold).
* Improvement: Some minor interface improvements.
* Improvement: More Color Genotypes options.
* Improvement: All the criteria are now available for the Branch & Bound II algorithm.
* Improvement: The CorrSum criteria was renamed as SA Corr (Sum of Adjacent Correlations) in the Options dialog box. Moreover, one can now choose to use the original Correlation (the one used in the Macintosh version of Mapmaker).
    The Correlation is (1 - r) (1 - EXP(-LOD)), where LOD is the true LOD score.
This option is activated when the check box "Use normalized LODs" is unchecked.
* Improvement: The Branch & Bound II algorithm now works recursively and will stop only when it finds the best order according to the given criteria.
* Improvement: More simulation options (missing data, data errors, F2 and SSD populations).
* Improvement: Pre-computing of RF matrices for ordering loci is now 2 times faster
* Improvement: Much faster execution of the BatchMap command (up to 4 times).
* Improvement: More simulation options.
* Improvement: Minor improvements.
* Improvement: Better importation of Mapmaker/EXP data files.
* Improvement: Simulation tool improved, with much faster AutoBatchMap and BatchMap commands. More genotypes (up to 508) allowed for BatchMap. Segregation distortion loci implemented (Backcross populations only). More comments. Option for generating semi-random marker positions. New command to display a histogram of the map sizes obtained.
* Improvement: the Import data command was re-written. It is now faster and more reliable. Also, it allows to import Mapmaker data that are not of the original format, ie, using symbols for genotypes others than A, B, C, D, H and -.
* Improvement: The main menu window interface was modified to allow locus numbers > 999 to be displayed correctly.
* Improvement: some minor things.
* Improvement: Added the two point and three point commands in the exported run file for Mapmaker/EXP when the Ripple command is included.
* Improvement: minor improvements.

* Bug fix: The Store data command was storing only the first 256 columns (version for Excel 2007 only).
* Bug fix: Some commands in Color genotypes were generating an error in case of having three (or more) co-segregating markers.
* Bug fix: Corrected a bug of double recombinant counting and display in Color genotypes.
* Bug fix: Some minor fixes.
* Bug fix: There was sometimes an error while importing .out Mapmaker/EXP files.
* Bug fix: The Replace order command was sometimes generating an error.
* Bug fix: Fixed some minor bugs introduced in the 1.7 beta version.
* Bug fix: The program was generating an error on the Mac OS X platform.
* Bug fixes: Many...
* Bug fix: Several minor bug fixes.
* Bug fix: A bug could occur when using the Read data command (with loci displayed in rows) with more than 254 genotypes.
* Bug fix: The Clear data command was crashing on Mac OS X.

* Interface: The "Option" dialog box was slightly re-organized.
* Interface: The main menu was re-organized.

v. 1.6 (October 11, 2006) - changes since v. 1.5:

* Feature: Added a SAD (Sum of Adjacent Distances) criteria for ordering, that corresponds to the old SARF. Note that using this criteria with sequences made of a mixture of loosely and tightly linked loci may not be a good idea, and that results may vary according to the mapping function selected (Haldane or Kosambi).
* Feature: Added an option to choose the space between linkage groups in "Draw all sequences" or "Draw pre-computed map" command.
* Feature: Bootstrap and Monte Carlo procedures to estimate and verify a sequence order. One can run both procedures using the command "Bootstrap order". To choose the Bootstrap procedure only, don't check the "Reshuffle initial order" check box when you are prompted for Bootstap parameters. To choose the Monte Carlo procedure only,  check the "Reshuffle initial order" check box and enter the value "100" in the field "Subsample size". To perform a combined test (Bootstrap + Monte Carlo at the same time), check the "Reshuffle initial order" check box and choose a value of Subsample size inferior to 100 (e.g., 95).
* Feature: Command "Show assignments" to display the assignments (or non assignments) to the declared sequences of all the loci declared in the Data window.
* Feature: Command to add the sequences of the current Framework map to the My Sequences field of the Main Menu window.
* Feature: Command to check for availability of new versions.
* Feature: Command to find the closest locus to a given locus ("Place locus...".
* Feature: Command to open saved linkage group sequences.
* Feature: Command to save current linkage group sequences.
* Feature: Command to show a graphical display of the extracted map from a database.
* Feature: Commands to open, save, import and draw the current framework map.
* Feature: Define a computed map as framework map.
* Feature: Drop locus. Useful to test the effect of removing loci one by one from a linkage group. Allows to quickly identify problematic markers. Similar to the Drop marker command of Mapmaker for Macintosh version 2.0. Note: a Perl script (written by Jean-François Rami) that adds this function to Mapmaker 3.0/EXP is available upon request from the Author.
* Feature: Exportation of Mapmaker/EXP .in file that can be launched within Mapmaker/EXP with the 'run' command.
* Feature: Extract marker positions from a personal database (a format is provided).
* Feature: F2 populations are now partially handled.
* Feature: If a new version is found at startup or as a result of the "Check version" command, a list of the last changes is downloaded and displayed.
* Feature: Importation of Mapmaker/EXP sequences (representing linkage groups).
* Feature: Importation of Mapmaker/EXP standard data files.
* Feature: Modified the SARF criteria. The SARF now really corresponds to the Sum of Adjacent Recombination Fractions (it was formerly corresponding to the SAD, or Sum of Adjacent Distances in centimorgans). The new SARF is more reliable than the old one (= SAD) when ordering a sequence made of a mixture of loosely and tightly linked loci.
* Feature: Partial handling for IRIL (Intermated recombinant inbred lines) populations.
* Feature: The Drop locus command now handles for F2 populations (codominant loci only).

* Improvement: "AutoOrder" will flip any sequence that starts with a locus number higher than the locus number it ends with.
* Improvement: "Draw QTLs" now can display marker names (Warning: QTLs with negative additivity are not displayed on the left of the chromosomes if this option is chosen).
* Improvement: "Options summary" in the Main Menu window is now displayed properly.
* Improvement: "Place locus" applied to F2 populations.
* Improvement: "Place locus" now shows the two closest markers instead of just the closest one.
* Improvement: "Sort map" in "Extract map from DB" has more output types.
* Improvement: Added 5 "Synonyms" columns in the marker database format.
* Improvement: Added a "Clear map" command in the pre-computed map window.
* Improvement: Added a button to directly access to Stored data in the Navigation Toolbar.
* Improvement: Added comments to the options cells in the ANOVA output windows.
* Improvement: Added the Bootstrap and Dop locus commands in the Commands toolbar.
* Improvement: Autofilter in the Show assignments window.
* Improvement: better behavior of stored data browsing.
* Improvement: Better behavior of the "Full screen" button.
* Improvement: better handling of data storage.
* Improvement: Better handling of the Quit command (Thanks to Jean François Rami, the VBA killer hacker).
* Improvement: better handling of Toolbars in case of several copies of MapDisto open at the same time.
* Improvement: Better handling of typing errors in the data files.
* Improvement: Disabled the automatic check for update at startup. Instead, the user can click on the "Check updates" button in the About window.
* Improvement: Displays an alert when importing a Mapmaker/EXP data file with wrong format.
* Improvement: Drawing maps is slightly faster (and nicer I hope).
* Improvement: Faster data export for WinQTLCartographer.
* Improvement: Faster display of Help section in Excel 2004 (Mac OS X).
* Improvement: In the ".in" file generated by "Export map..." with the Options set to export for Mapmaker/EXP, the mapping function follows the one chosen in Options.
* Improvement: in the Options dialog box, the "Options for r custom" are activated only if the "Custom" radio button is selected.
* Improvement: in the Options dialog box, the radio box "Use absolute distances" is  activated only if the "GraphGenot" radio button is selected.
* Improvement: It is now possible to work with up to 1,000 sequences.
* Improvement: It's now possible to import Mapmaker/EXP data files that have up to 504 individuals. Works with Excel X and 2004 for Mac OS X, and Excel 2003 for Windows. Should work with Excel XP (2002). With Excel 2000, only the marker data are imported properly, QTL data are cut.
* Improvement: Many computations are faster (up to 2 times) (Except for F2 populations).
* Improvement: Many computations are faster (up to 2 times) for F2 populations.
* Improvement: More advanced saving of graphical maps & QTLs.
* Improvement: Several minor interface modifications.
* Improvement: Small interface improvements.
* Improvement: The "Open" and "Save" sequences now handle for sequence names (previously save sequences are not compatible with this new version).
* Improvement: The exported map and data files for WinQTLCart, QGene and MapQTL are now saved in the folder than contains the running MapDisto copy.
* Improvement: The LOD min and r max values in the "Options" dialog box are now taken as default values in the "Find groups" command.
* Improvement: The user is now prompted to choose the source/destination folder in the Importation/Exportation procedures.
* Improvement: Updated Help.
* Improvement: Updated the Help section.
* Other minor improvements.

* Bug fix: "Check update" was sometimes generating an error on Windows platform.
* Bug fix: "Compute tables" now displays correctly the two-point LOD score values for F2 populations.
* Bug fix: "Draw QTLs" now works properly for F2 populations.
* Bug fix: "Find groups" could be wrong when R.F. was > 0.5.
* Bug fix: "Find groups" was not taking the "r max" parameter into account, due to an Excel bug (in the VBA compiler?). I found a way to overcome the problem, but Microsoft is welcomed to fix the following [serious] issue:
    The condition "a <= b" is not equivalent in VBA to the condition "a - b <= 0".
* Bug fix: "Place Locus" was working improperly in some cases.
* Bug fix: "Store data" now stores quantitative trait(s) data.
* Bug fix: Additional fix for the Cancel issue in Automap.
* Bug fix: Click on Cancel in the Automap and AutoOrder commands was problematic.
* Bug fix: Click on Cancel in the Boostrap command no longer clears the Bootstrap results window.
* Bug fix: Corrected small bug in data export for Mapmaker/EXP 3.0.
* Bug fix: Dragging a complete sequence to the right no longer generates loss of the last loci in the sequence.
* Bug fix: Drawing QTLs wasn't displaying a QTL linked to the first locus of a linkage group.
* Bug fix: Drawing QTLs with a single linkage group works faster and doesn't draw extra lines.
* Bug fix: Fixed a bug in the Remove Toolbars command in the Troubleshooting section of the Help.
* Bug fix: Fixed a small bug in the sorting process on an extracted map.
* Bug fix: In "Import sequences", the current sequences could be erased in some cases.
* Bug fix: in "Segregation chi2" and "QTL/ANOVA1" commands, the genotypic classes are now displayed correctly.
* Bug fix: In 'Find groups", the "Use all loci" option was disabled in some cases.
* Bug fix: In 'Find groups', the last marker was omitted if the command was ran for any other sequence than 'All loci'. Fixed.
* Bug fix: In some very rare cases, the F-test associated probability computation was  generating an error 2036.
* Bug fix: In the Detailed map command, the computation of the LOD score statistic was false for all population types except F2s.
* Bug fix: The Delete results command now completely erases the ANOVA window.
* Some other small bug fixes.

* Misc.: Corrected inappropriate text in an Export dialog box.
* Misc.: reorganized internal code.
* Misc.: the option to work with loci names was deactivated, until I find a way to display the results in a legible way.

v. 1.5 (October 11, 2006) - changes since v. 1.4:

* Feature: Draw QTLs on the graphical map (One trait analysis).
* Feature: Draw QTLs on the graphical map (All traits analysis).

* Improvement: Faster and more accurate map drawing, especially on Windows systems.
* Improvement: the 'Draw all sequences" commmand now behaves exactly as the 'Draw map' command.
* Improvement: It's now possible to define the maximum distance for linkage groups searching as a distance in centimorgans.
* Improvement: Slight interface modification for data management.
* Improvement: It is now possible to rename the MapDisto file (e.g. to append the name of a mapping project), thus to have several copies open at the same time.
* Improvement: Slight improvement in QTL drawing.

* Bug fix: under some conditions, 'Auto Order' was erasing the working sequences. Fixed.

v. 1.4 (October 11, 2006) - changes since v. 1.0:

* Feature: Export data and map for WinQTLCartographer 2.5 and higher (Excel format).
* Feature: Better export for QGene. Now its automatically exports the map and the data files as text files, ready to use in QGene.
* Feature: Added warning message for the "Export map" command that reminds the user that the "Write map" has to be ran first before exporting a map.

* Improvement: "Export Map" no longer needs to run "Write map" before. Export for MapQTL and QGene has been modernized.

* Bug fix: "Find Groups" didn't compute again the recombination fraction matrix when the data were read again.
* Bug fix: "Export data as .raw" for Mapmaker was not working properly when there was missing data in quantitative traits.
* Bug fix: "Object required" message while exporting a map for MapQTL and GraphGenot.
* Bug fix: Fixed two small bugs in the dialog boxes for choosing the sequences.

* Correction: assignation of the geneotypic classes to a, b, c and d classes was corrected in this Help/Data analysis menu (thanks to Peter Wehling).

* Misc.: The option to choose the font for marker labels and distances in 'Options' is now functional.

* Accelerated ANOVA1 command.
* modernized the dialogboxes for choosing sequences and traits.

* fixed a small bug in the Options values that was affecting the DrawMap command.
* improved the Use these Data command.

* fixed a small bug in ANOVA display.

* new user-friendly interface for options.

* Accelerated execution of the following commands: Draw map, Draw all sequences, Draw pre-computed map, Compute tables, Find Groups, Segregation c2, Detailed map, Order sequence, Ripple order.
* Added a Data+ sheet that allows to handle for up to 508 markers or loci.
* Now you can assign names to the sequeces you are working with.
* Likelihoods of orders are computed and may be used as a criteria for ordering loci (based on two point estimates; may deviate significantly from multipoint likelihoods).
* Added a command for cleaning the current working sequences.
* Many bug fixes.

* You can now store more than one data set. When you are in the 'Data' window, use 'Store data' command to store your current data in a new sheet. You can navigate in the different data sheets you have generated using the left and right arrows.
* Small bug fixes.
* Minor interface changes. Parameters for data have now to be entered in the 'Data' Window.
* Minor interface changes. Parameters for data have now to be entered in the 'Data' Window.

Three new functions:.
* AutoOrder: Automatically orders and computes all declared sequences.
* Draw all sequences: Automatically draws all declared sequences.
* AutoMap: Automatically finds linkage groups, orders, computes and draws all linkage groups.

* Color mapping! Enjoy having loci of different colors according to their names. See 'Draw Pre-Computed Map' paragraph in 'Data Analysis' section of this help.
* 'Draw Pre-Computed Map' displays better Absolute distances.
* You can now choose the font size in the 'Draw Map' and 'Draw Pre-Computed Map' commands (in "Options" window).
* Added a 'Replace Order' command in output windows of 'Ripple', 'Compare all orders, and 'Order' commands. This command will replace the current sequence by the output sequence instead of adding the output sequence after all listed sequences in the main menu.
* Added an option for better display in MacOS and Windows. See 'Options' in the Commands window.
* Minor changes in the 'Quit' command (thanks to Jean François Rami).
* Work progress is now displayed in the Status Bar (better compatibility with MacOS X platform).
* Other cosmetic interface changes.

* Finalized the function for ordering sequences.
*Added a function for verifying local orders ('Ripple order').
*Added a function to reverse a given sequence, eg sequence 1 2 3 4 is changed to sequence 4 3 2 1 ('Reverse order').
*Re-organized the Main Menu window for a better interface.
*Renamed commands: 'Order' changed to 'Order sequence'; 'Compare' changed to 'Compare all orders'.

* Added an option for exporting a writed map for MapDisto (that is, for MapDisto) in order to facilitate the drawing of the maps of all sequences at the same time.
* Added a 'Quit' button which makes easier to work with several copies of MapDisto (in different folders or directories) in removing the 'Toolbars' problem (see section 'Problems').

* Added support for large linkage groups in 'Find Groups' command.

* Corrected a bug introduced in v. leading to false linkage groups in 'Find Groups' command.

* New option for exporting RFs tables in a text file in 'Compute tables' command  (useful for sequences with more than 254 loci).

* New 'Export data' command for exporting your data as a Mapmaker-compatible .raw text file.

• 'Find Groups' now works for all sequences, ie. you can search for linkage groups in a declared sequence (it was previously limited to sequence 99, ie. all loci). It no longer finds linkage groups with zero loci. The 'Copy sequences' no longer copies empty groups.

• Corrected a small bug in LOD score computation under very rare situations.
• Fixed errors in work progress displays.

New functions:.
* New  'Compare' and 'Order' commands for ordering loci. Attention: the 'Order' command is not finalized, and is just provided for having a preview of the final function.
* New 'QTL/ANOVA1' command for finding QTLs.

Major improvements:.
* Now handles for SSD and DH populations.
* New command for drawing maps computed by other software.
* More options for drawing maps. Maps are cleaner.

Minor improvements:.
* Data can now be arranged with loci and traits in rows or columns.
* Data no longer need to be numerical values only.
* You can now export maps for MapQTL.
* You can now enter up to 97 different sequences.
* Buttons for copying sequences from 'Find Groups', 'Compare' and 'Order' commands in 'Your sequences'.

Many bug fixes.

Interface improvement (I hope).

* Temporarily removed bugged option for finding linkage groups from other sequences than the sequence made by all loci.
* Added an 'Options' window which removes some borrowing dialog boxes.
* In 'Draw map', declaring a wrong sequence number no longer generates an error.
* Corrected a small bug causing an incorrect drawing of the first locus of a map.
* Added a function for drawing genetic maps ('draw map').
* Added a field for defining a default sequence to test.
* The 'Cancel' buttons are now functional.
* Added indication of progress of computations and writing operations in the main menu.
* Added a 'version history' field in the 'Help' menu.
* Added a 'Problems' field in the 'Help' menu.
* Added two Excel command bars which replace the navigation menu and which give the different commands always available.
* Added a navigation menu.