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Arlequin 2.001

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The present release of Arlequin is a maintenance version

It comes with only two files : arlecore2001.exe and arlecore2001.jar

You still need to proceed to the installation of Arlequin ver 2.000 
BEFORE 
downloading these patched files

These files are updated versions of arlecore.exe and arlequin.jar that are present in the release of Arlequin ver 2.000. They correct several bugs that were detected by the users of Arlequin 2.000. Most of these bugs were present in the arlecore.exe file.

Installation:

1. After extraction, simply copy these two files in the directory where you installed Arlequin 2.000.
2. Rename your copies of arlecore.exe and arlequin.jar to arlecore2000.exe and arlequin2000.jar
3. Make copies of arlecore2001.exe and arlequin2001.jar and rename them to arlecore.exe and arlequin.jar

That's it !

Modifications:

The present version of Arlequin does not implement any new method that was not present in ver. 2.000. It is only aimed at fixing annoying bugs.

Improvements:

1. The computation of haplotype frequencies is now much faster, especially when there is a large number of polymorphic loci involved. All computations based on the EM algorithm should then be faster.
2. Cosmetic changes have been made in the output of Arlequin.

Main fixed bugs:

1. The automatic creation of Arlequin projects wrote key words in a wrong order, causing some projects to be impossible to read by the Arlequin interface.
2. Genepop conversion utility has been made more compatible (but there are still some problems)
3. Minimum spanning tree structure generated in NEXUS format could not be read if sample names contained white spaces.
4. Genotype likelihoods were not correctly computed in the genotype assignment procedure.
5. External distance matrices could not be read if the key word LabelPosition=LINE was not explicitly stated.
6. Fct p-value was not correctly estimated for the locus-by-locus Amova.
7. Computed heterozygosity was not correctly estimated when haplotypes with zero frequency were present.
8. AMOVA: P-values were generally not well estimated for small sample sizes or small number of populations. This was because of rounding errors when comparing observed and randomized F-statistics.
9. Mismatch distribution: Upper and lower bounds for the mismatch distribution were not correctly computed
10. Comments within groups structure did not allow samples to be read and project to load correctly.
11. Computations of genetic distances taking into account population size difference caused Arlequin to crash when one population was monomorphic.
12. The mean of the mismatch distribution did not always correspond to the mean number of pairwise differences computed under the molecular diversity indices section. This was due to the fact that one had the impression that one could select different distance for the mismatch, while only the number of pairwise differences is always computed for the mismatch.
13. Unable to export Arlequin projects into other format. This problem occured when when there were trailing blanks or tabs at ends of lines.

Remaining problems:

1. For microsatellite data, it is still possible to select a molecular distance other than the No. of different alleles, even though it is always this distance that is computed.
2. Missing data level is not taken into account when computing AMOVA locus-by-locus, because all the missing data are automatically suppressed.
3. Missing data are treated as an allele when estimating haplotype frequencies.
4. Some minor inconsistencies may persist in the interface (e.g.: an unnecessary large number of permutations are set by default (100,000) for the likelihood ratio test of linkage disequilibrium, while a smaller number (1,000) would be enough)
5. The collection of summary statistics in batch file is still imperfect.
6. There is still no support for the Java JRE 1.2 or more recent.
7. There is no arlequin2001.exe patch version available for the Linux version.

Why are there remaining problems?

TIME !!! I have only one life and cannot find the time to make all the modifications I would like. Also, my colleague and friend S. Schneider has joined the dark side of the universe (the industry), and I am alone to take care of Arlequin by now. This is the reason why the java interface has not changed and why there is no new Linux version available.

In the future, there are thus chances that only a Windows version will be made available.

Current download statistics:

For information purposes, here are the statistics concerning the downloads made on our server between March1st  2000 and  January 13 2001.

Arlequin item	Downloads	Bytes
Win32 version	13,324	26,470,763,871
Mac OS version	2,404	20,532,915,158
Linux version	348	1,456,274,789
Manual	21,130	2,710,557,729

No new arlecore.exe Linux version ?

That is correct. Unfortunately I did not find the time (or the people) to implement that version. Sorry.

Enjoy...

Laurent Excoffier

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18 January 2001

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What is new in Arlequin 2.000 compared to 1.1

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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 F_S 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.
9. New user manual

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Last minute changes

• New installation procedure for the Linux version. 
• Java interface has been updated (prettier) as compared to that shown in the manual

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31 March 2000