JoinMap 4 & 4.1 Release notes
=============================


=== 31 July 2013 ===
Maintenance releases of JoinMap 4 and 4.1
  (Build: 31jul13.4feb11)

= A function is added to the Grouping node menu:
  'Assign Identical Loci to Their Groups'. The procedure to
  create a grouping node (see 6 and 19 March 2013) assigns
  sets of identical loci to group number 0, with the
  exception of one representing locus for each set. The new
  function will assign the identicals with group number 0 to
  the groups of their representing loci.


=== 19 March 2013 ===
Maintenance release of JoinMap 4
  (Build: 19mar13.4feb11)

= The same changes are applied to JoinMap 4 as in the recent
  maintenance release of JoinMap 4.1 of 6 March 2013.
  See below.


=== 6 March 2013 ===
Maintenance release of JoinMap 4.1
  (Build: 6mar13.4feb11)

= The grouping procedure of sets of loci into linkage
  groups used to be limited to sets of roughly 4000 loci due
  to available RAM memory. As the program is 32-bit it is
  limited by the maximum addressable amount of RAM. A new
  algorithm is implemented that is designed to store
  intermediate results on hard disk rather than in RAM. The
  program can now accommodate sets of up to ~50,000 loci,
  while keeping computation time within acceptable limits.
  On a typical present-day PC, the grouping procedure of
  50,000 loci takes about one hour. The speed of the hard
  disk is an important limiting factor. As the computations
  scale quadratically with the number of loci, groupings of
  smaller sets are still quite fast: 10,000 loci in about
  three minutes, 5000 loci in just about twenty seconds and
  1000 loci in a second.

  Beware that such oversized datasets require extreme file
  sizes: the 50,000 loci require a file of ~30 GB for the
  pairwise data. When creating the grouping node and group
  nodes, this file with pairwise data will be duplicated.
  Thus, ensure that the hard disk in use has sufficient free
  space when dealing with such datasets.

  In large datasets there will often be some redundancy (in
  fact, in most cases there should be). As an new feature
  the grouping procedure determines which loci are
  identical. Being identical is based on the entire set of
  genotype observations of all included (not excluded)
  individuals, including the missing observations. Sets of
  identical loci will be represented by one of them (the
  first not excluded locus). Identical loci will be
  specified at the bottom part of the 'Groupings (text)'
  tabsheet, while a numerical summary is given with the blue
  'Further information' tool bar button. One advantage is
  that the pairwise data will only be calculated for the
  loci that represent their identicals, thus reducing the
  computations.

  When determining a grouping node and group nodes, only the
  representing loci of sets of identical loci will be
  grouped, while in the grouping node tabsheet the identical
  loci will automatically obtain group number 0 (i.e. will
  not be part of a group), with 'identical' as Node name.

  The determination of the SCL-Values takes the identicals
  into account and will list 'identical' as SCL-Value to
  link them to their representing locus. The
  representing loci will obtain a regular SCL-Value.

  The procedure 'Assign Ungrouped Loci to SCL-Groups' will
  leave the identicals assigned to group 0.

  The procedure for determining a grouping based on a map or
  another grouping node will take the identicals into
  account and assign them to group 0.

  The grouping procedure may also be done based on the
  recombination frequency or the linkage LOD. For
  population types CP, DH and HAP, this means that the
  linkage phases must be determined to obtain these values.
  In the original procedure the pairs were sorted to their
  independence LOD value prior to the linkage phase
  determination. To be able to deal with very large datasets
  this sorting is not done anymore. The independence LOD
  threshold for pairs subject to phase determination, which
  used to be internally set at a LOD value 1.0, is now a
  Calculation Options parameter at the Population tabsheet:
  'Determine linkage phases ...'. When in doubt about the
  linkage phase determination you can increase this
  parameter value.

= The navigation panel could disappear after resizing it to
  the smallest size (by dragging the splitter between the
  navigation and the contents-and-results panel).
  Disappearing is now prevented.


=== 11 June 2012 ===
Maintenance release of JoinMap 4
  (Build: 11jun12.4feb11)

= In text tabsheets, like the 'Map (text)' tabsheet,
  sometimes a non-printable character got inserted at a
  random position (visible as a square character). It
  prevented copying the area around it. It is corrected.


=== 14 March 2012 ===
Maintenance releases of JoinMap 4 and 4.1
  (Build: 14mar12.4feb11)

= For population types DH, HAP and CP, the Linkage LODs for
  the Groupings (text and tree) tabsheet as well as the
  corresponding SCL-values of derived Grouping nodes were
  calculated erroneously. This is corrected.

= The calculation option 'Determine linkage phases (CP, DH,
  HAP) with a LOD larger than' was reset to the value 1.0
  each time the groupings of a population node were
  (re)calculated. This is corrected.


=== 4 August 2011 ===
Maintenance release of JoinMap 4.1
  (Build: 4aug11.4feb11)

= The Population-menu functions 'Exclude Identicals' and
  'Exclude Similar Loci' could lead to runtime errors with
  larger datasets. The functions have been recoded and are
  now also much faster.

= Renaming the project file without renaming the project
  directory would lead to a rewritten, empty project file.
  This is corrected.


=== 3 August 2011 ===
Maintenance release of JoinMap 4
  (Build: 3aug11.4feb11)

= The Population-menu functions 'Exclude Identicals' and
  'Exclude Similar Loci' could lead to runtime errors with
  larger datasets. The functions have been recoded and are
  now also much faster.

= The following minor errors were corrected:

  The heading in the Genotype Probabilities tabsheet had
  'R.Genotype' instead of 'Genotype' for the central
  genotype.

  Long group and map node names were made shorter than the
  allowed 20 characters when closing the project.

  Map charts would inexplicably draw some 'homologs' lines
  between loci that did not have identical names.

  The simulated annealing sometimes appeared to continue
  too long.

  For map nodes the 'Info on Tabsheet Contents' button and
  function in the File-menu should be active for several
  tabsheets while they were not.

  Any fixed order used in the determination of plausible
  orders was not reported in the
  'Info on Tabsheet Contents'.

  The name of the HTTP Host of the proxy settings in the
  environment options was not saved.

  Sometimes the decimal separator (the point) was reset to
  the preference in the MS-Windows Regional Options. This
  would lead to error messages like
  '0.000 is not a valid floating point value'.

  Renaming the project file without renaming the project
  directory would lead to a rewritten, empty project file.


=== 20 July 2011 ===
Final version of JoinMap 4.1
  (Build: 20jul11.4feb11)

= The only, but very important, enhancement of version 4.1
  of JoinMap is the ability to use the multipoint maximum
  likelihood mapping algorithm on populations of type CP,
  i.e. the outbreeding species full-sib family. The new
  method is described in a paper that was accepted for
  publication:

  Van Ooijen, J.W. (2011). Multipoint maximum likelihood
    mapping in a full-sib family of an outbreeding species.
    Genetics Research, accepted June 2011.


=== 7 February 2011 ===
Maintenance release of JoinMap 4
  (Build: 7feb11.4feb11)

= The Colorize function to show graphical genotypes now
  takes the linkage phases into account for DH and HAP
  population types. For instance, genotype a of a marker
  with phase {1} is shown in the same color as genotype b
  of a marker with phase {0}.

= A function was added to work on the Similarity of Loci
  tabsheet: Population-menu > Exclude Similar Loci.
  It works like the Exclude Identicals function, but instead
  of using a similarity value of 1.0 this function prompts
  for a similarity value to use. If two loci have a
  similarity above the given value, the second locus will be
  excluded on the Loci tabsheet, unless the first locus is
  already excluded (to prevent excluding locus C if locus B
  is similar to locus A, and locus C to B but not to A).
  This function allows spatial sampling of the loci.

= The grouping process was given a somewhat higher speed.


=== 6 October 2010 ===
Maintenance release of JoinMap 4
  (Build: 6oct10.9feb10)

= In recent maintenance releases JoinMap was set to use
  Windows Desktop Themes. Several users experienced runtime
  errors due to this. The use of themes by JoinMap is
  stopped.

= Clicking on the 'no data' header of an empty Data tabsheet
  resulted in an 'OLE error' message. This is repaired.


=== 20 April 2010 ===
Maintenance release of JoinMap 4
  (Build: 20apr10.9feb10)

= When creating maternal and paternal population nodes of a
  CP type dataset node, now loci with a <hkxhk> segregation
  type are also exported, unless the classification type is
  (hh,k-) or (h-,kk). The genotypes hk, h- and k- are all
  exported as unknowns --; genotypes hh and kk are exported
  as ll and lm, respectively, for the first (=maternal)
  parent, and as nn and np, respectively, for the second
  (=paternal) parent.


=== 19 Februay 2010 ===
Maintenance release of JoinMap 4
  (Build: 19feb10.9feb10)

= Creating a population node of a CP type dataset node
  resulted in an error. A similar bug resulted with the
  exporting as loc-file from Data tabsheets in minor
  errors in the loc-file. The bugs were repaired.


=== 16 Februay 2010 ===
Maintenance release of JoinMap 4
  (Build: 16feb10.9feb10)

= To make working with large marker datasets of a population
  a bit faster, new options are introduced:
  -A checkbox option on the tool bar controls whether or not
  the various Data tabsheets are loaded; it can also be set
  in the Options-menu.
  -Large datasets create huge tables of pairwise linkages
  and if they are not going to be inspected things are
  faster if the tables are left out altogether. Therefore,
  in the Group tabsheet of the calculation options two new
  checkboxes control whether or not weak and strong linkages
  tables are created when the linkages are calculated.

= The Colorize function to show graphical genotypes now
  takes the linkage phases into account (if available) for
  all segregation types except <hkxhk>. For instance,
  genotype lm of a marker with phase {1-} is shown in the
  same color as genotype ll of a marker with phase {0-}. The
  default colors are modified for a better correspondence
  between the segregation types.

= An option is added that controls whether the current
  selection or the entire tabsheet contents must be printed,
  copied, or exported; it is a check box on the tool bar and
  is also available in the Options-menu.

= The Highlight Errors function now also allows
  classification types (a,h) and (h,b) for population types
  BCpxFy. And when the y-generation is zero (i.e. it is a
  normal BC1), only genotypes a and h (BCAxFy), or h and b
  (BCBxFy) are allowed.

= With an added option in the Help-menu you can now check
  via the internet whether a newer release is available.
  If your internet connection requires the use of a proxy,
  you can supply the proxy name and port in the environment
  options.

= Several internal actions that may take a while now change
  the cursor temporarily into the hourglass cursor.

= Map-files or pwd-files in which the comma is used as
  decimal separator (instead of the point) will be loaded
  correctly.

= Maps with multiple linkage groups are now inverted
  group by group with the Invert Map function of the
  Map-menu.

= The time stamp now also shows the seconds.


=== 11 August 2008 ===
Maintenance release of JoinMap 4
  (Build: 11aug08.7apr08)

= In the ML mapping algorithm the fixed order was not always
  maintained; this is corrected.

= The tabsheet with the Locus Means of the Genotype
  Probabilities is sorted on the map position of the loci.
  This will result in a proper chart when plotted against
  the map position.

= The tabsheet with the Individual Means of the Genotype
  Probabilities is given in the original order of the
  individuals.


=== 23 July 2008 ===
Maintenance release of JoinMap 4
  (Build: 23jul08.7apr08)

= If the grouping cannot be calculated for a population
  type CP, better information will now be shown.

= The situation with three (or more) loci at the same map
  position could lead to a floating point error in the ML
  map calculations. This is corrected.

= The cooling control parameter of the ML Mapping algorithm
  had a lower limit of 0.001 which is now reduced to
  0.00001; the upper limit is now set to 1.0.

= The tabsheet with the Locus Means of the Genotype
  Probabilities now also shows the map position of the loci.

= When no project is open, pressing the OK button on the
  Environment and the Calculation 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.


=== 8 April 2008 ===
Maintenance release of JoinMap 4
  (Build: 8apr08.7apr08)

= For a BCpxFy the genotype probabilities given the map
  given two heterozygous or dominant flanking markers were
  not completely right. This is corrected.

= The map chart options dialog can be opened when no map
  chart is visible; changing the options will have the same
  effect as 'Save as Default Map Chart Options'. Any future
  map chart will be drawn according to these options.

= Also, when no map chart is visible the 'Reset to Preset
  Map Chart Options' can be activated, which will affect
  all future map charts.

= The loading of MAPMAKER raw data is slightly improved.

= Various minor (internal) improvements were made.


=== 4 May 2007 ===
Maintenance release of JoinMap 4
  (Build: 4may07.4oct06)

Changes:
= JoinMap 4 was enabled to run under Windows Vista.
  For installation of the user license under Windows Vista,
  please see the 'Installation ReadMe' file on the CDROM or
  in the program directory after running the program
  installation 'setup.exe'
  (typically: 'C:\Program Files\JoinMap4').


=== 18 April 2007 ===
Maintenance release of JoinMap 4
  (Build: 18apr07.4oct06)

Changes:
= When exporting the Data tabsheet of a Map node of a CP
  type population as a loc-file, the map position of
  markers was given at the wrong place in the file.
  This is corrected.

= The exporting of a Dataset tabsheet of a Dataset node as
  a loc-file did not function properly. This is corrected.


=== 5 March 2007 ===
Maintenance release of JoinMap 4
  (Build: 5mar07.4oct06)

Changes:
= When calculating the linkages for groups of population
  type CP, it is possible that the linkage phases cannot
  be determined and thus also no recombination frequencies
  can be calculated. In such instances the program could
  generate an unclear runtime error message: 'unknown error
  in sclastype()'.
  This problem is corrected and the information given in
  the 'Info on Tabsheet Contents' has become more complete
  about the linkage phases determination status.


=== 4 October 2006 ===
Maintenance release of JoinMap 4
  (Build: 2oct06.4oct06)

Changes:
= For extremely large values of the chisquare distribution
  the P-value in the Grouping tabsheet could not be
  calculated and resulted in the freezing of the program.
  The P-value is calculated irrespective of the Grouping
  parameter chosen.

  A new algorithm to calculate the P-value is now used.

= For very large linkage groups the computations of the
  linkages may appear to take extremely long. Actually,
  it is not the computations that take a long time but
  the loading of the resulting data into the Linkages
  tabsheets. For such large linkage groups there may
  be very, very many pairs to display on the Weak and
  Strong linkages tabsheets, depending on the chosen
  corresponding thresholds.

  To allow for more precision here, the recombination
  frequency thresholds on the Group tabsheet of the
  Calculation Options now have up to four decimals.

  Unfortunately the loading of the data into the
  tabsheets cannot be shown on the progress bar, but the
  progress of the program is now shown with some simple
  comments on the status bar:
    'loading table "Weak Linkages"'
    'loading table "Strong Linkages"'
    'loading table "Suspect Linkages"'
  together with the numbers of rows that must be loaded,
  allowing the user to see and estimate the progress.
  These comments are usually only visible with very large
  groups.


=== 25 July 2006 ===
Final edition of JoinMap 4
  (Build: 25jul06.16jun06)