What is new in Arlequin 2.000 compared to 1.1

  1. Several bug corrections.
  2. An entirely redesigned user interface written in Java.
  3. Support for the Windows 9X/NT/2000, MacOS on GX/Power PC processors, and for the Linux/Intel platforms. Windows 3.1 is not supported anymore.
  4. Several new population genetics methods have been added or improved
    1. Locus-by-locus AMOVA. Useful when there is a lot of missing data.
    2. Implementation of Fu's FS test of selective neutrality. Its significance testing is achieved through coalescent simulations.
    3. Computation of Nei's  mean number of pairwise differences within and between populations. Raw and corrected distances are available at the inter-population level.
    4. Computation of genetic distances between populations taking into account unequal effective population sizes
    5. Computation of a Minimum Spanning Network from a matrix of distances between haplotypes. Tree output in Nexus format.
    6. Mantel test. Computes the correlation or the partial correlations between 2 or 3 matrices, and test their significance by permuting rows and columns in one or two matrices.
    7. Assignment of genotypes to populations. For each genotype in the sample, we compute its likelihood assuming that it belongs to different populations.
    8. Mismatch distributions are now fitted to the observations by a generalized-least square procedure instead of using a moment estimator. We also compute a test statistic of the validity of the estimated demographic expansion. We provide percentile confidence intervals around the expected mismatch that contain a given percentage of the mismatch distributions simulated around the estimation.
    9. Tajima's D P-value is now obtained by coalescent simulations.
  5. Result files are now in HTML format, and accessible through a web browser. One can easily navigate between different sets of results and between portions of the result files through a document tree appearing in a separate pane. The web browser is automatically launched after each run of Arlequin.
  6. The references of each method used by Arlequin are now provided in the result file.
  7. Allows different log files for each project.
  8. An external text editor and web browser have to be selected for having access to the projects and result files, respectively.