# What's New

This page describes the additions (NEW), changes (CHG) and bug fixes (BUG) that have been made to OptiMAS in recent versions.

#### New in version 1.5 (September 1st 2014)

- NEW: Computation of linear or non linear indexes combining any of the information available (QTL, predicted values, molecular scores, quantitative traits...) to facilitate decision making.
- NEW: Allelic effects. It is now possible to add a file with QTL additive allelic effects. When this file is provided, OptiMAS uses this information to compute predicted genotypic values.
- CHG: Input files format changed. Although the previous input files format is still supported by OptiMAS 1.5, we recommend to use the new input files format (see the documentation for OptiMAS 1.4 here to have a description of the old input files format):
  The new map file format does not include informations on QTLs and favorable alleles any more, and is therefore totaly similar to Flapjack format.
  Two new QTL files are supplied by the user to (i) specify the information regarding the QTL position and identification of favorable alleles, and (ii) define the QTL region, meaning affiliate a set of marker that will be used to compute the allele transmission.
  Users can now (optionally) include quantitative traits in the genotype/pedigree file.
  As OptiMAS now manage several kinds of scores, some columns have been renamed (Weight => MS_Weight, UC => MS_UC).
  See data preparation section and sub-sections.
- CHG: Algorithm modifications allow a larger number of flanking markers and/or parental alleles.
- CHG: The markers present in the genotype/pedigree file can be unordered.
- CHG: QTL columns show the real QTL names (those found in QTL input files).
- CHG: Columns masking within the step1 main table now automatically affects step2 and step3 tables.
- BUG: Cut-off on diplotypes could cause, under special conditions, a slight bias in the computation of the molecular score (MS).
- BUG: Fixed inoperant "drag and drop" of individuals between two crosses lists (step3 tables).
- BUG: Color visualisation issue fixed.
- BUG: Others minor bugs fixed.

#### New in version 1.4_13.01.24 (January 24th 2013)

- CHG: Stability reinforced.
- CHG: OptiMAS algorithms have been improved. We focused essentially on the optimization of the time and the memory consumption. For example, a new parameter “cut-off gametes” has been added. It corresponds to the probability that the number of crossovers expected in the region between flanking markers exceeds a given value. Thus, unlikely gametes with number of crossovers over this value are removed and no more considered in subsequent computations. Besides speeding up time calculation, it allows users to select more surrounding markers for the computation of the genotypic probabilities at QTL positions (very useful in a multi-allelic context).
- CHG: Residual heterozygosity for founder parents of the selection programme has been managed.
- NEW: A new module (integrated within the GUI menu bar) has been developed to check the consistency of the marker genotyping information along generations of selection. Individuals having genotype data inconsistent in light of their ancestry (genotyping error or an error in the declared pedigree) are filled with missing data.
- NEW: Previous analyses run via the command line version or the GUI can be reloaded with the precedent configuration/preferences (weights, cut-offs, colors…).

#### New in version 1.3_12.10.10 (October 10th 2012)

- CHG: Algorithm improved (v1.1, v1.2, v1.3). OptiMAS run significantly faster (6-7 times compared to v1.0 with "blanc" dataset - the gain increases with the complexity).
- NEW: OptiMAS available for GNU/Linux, Windows (XP/7) and Mac OS X (10.5 or later) systems (see Download page).
- NEW: Residual heterozygosity for founder parents of the programme can be managed and declared at markers (not QTL), however using this option should be discouraged due to loss of information.
- CHG: Offline and online help/documentation support (website created).
- NEW: Weigths and colors/cut-off can be saved then reloaded.
- CHG: new way to calculate the "Utility Criterion" (see Results & Output files section).
- NEW: QTL complementation selection procedure (QCS, see Step 2).
- NEW: Factorial design (two lists of selected individuals can be crossed together, see Step 3).
- BUG: Reload previous analysis with modified lists of selection/crosses.
- BUG: Import data (browse input files with "complex" names).

#### New in version 1.0_11_09_21 (September 21th 2011)

- CHG: Algorithm improved. OptiMAS run significantly faster (2-3 times).
- NEW: Manage customized Flapjack input files (map & genotype/pedigree).
- NEW: Graphical interface changed (Import Data).
- NEW: 2 examples data sets (biparental / multiparental) integrated within the software procedures.
- NEW: Offline help/documentation.
- NEW: Output file table (tab_check_diplo) to check that results are sustainable and identify if too many phased genotypes were removed.
- NEW: Filtered view for QTL (columns), Individuals (rows) and cycle/group selection ("view" button in step 1).