[Genetics] [Fwd: Other: Software Arlequin ver 3.1]

[Tanja Pyhäjärvi]

-------- Original Message --------
Subject: 	Other: Software Arlequin ver 3.1
Date: 	Thu, 21 Sep 2006 03:18:44 -0400 (EDT)
From: 	evoldir at evol.biology.mcmaster.ca
Reply-To: 	brian at helix.biology.mcmaster.ca
To: 	tanja.pyhajarvi at oulu.fi



Please note that a new version (3.1) of Arlequin is now available on

http://cmpg.unibe.ch/software/arlequin3

Compared to version 3.01, Arlequin 3.1 includes several cosmetic and
speed improvements, as well as bug corrections and additional features:

Improvements
------------
* Locus-by-locus AMOVA can now be performed independently from
   conventional AMOVA. This can lead to faster computations for
   large sample sizes and large number of population samples.
* Faster routines to handle long DNA sequences or large number
   of microsatellites.
* Faster reading of input file.
* Faster computation of demographic parameters from mismatch
   distribution. Improved convergence of least-square fitting algorithm.

Additions:
----------
* Computations of population specific inbreeding coefficients and
   estimation of their significance level.
* Output of the number of alleles as well as observed and expected
   heterozygosity per locus for all populations.
* Computation of the Garza-Williamson statistic for MICROSAT data.
* New sections are provided at the end of the result file, in order to
   report summary statistics computed for each population:
     - Basic properties of the samples (size, no. of loci, etc...)
     - Heterozygosity per locus
     - Number of alleles + total no. of alleles over all pops
     - Allelic range + total allelic range over all pops (for
       microsatellite data)
     - Garza-Williamson index  (for microsatellite data)
     - Number of segregating sites, + total over all pops
     - Molecular diversity indices (theta values)
     - Neutrality tests summary statistics and p-values
     - Demographic parameters estimated from the mismatch distribution
       and p-values.
* New shortcuts are provided in the left pane of the html result file
   for F-statistics bootstrap confidence intervals, population specific
   FIS, and summary of intra-population statistics.

Bug corrections:
----------------
1.  Locus-by-locus AMOVA failed for on DNA sequences when corrections
     for multiple hits were selected. These corrections have been di
2.  File conversion towards the Phylip format could not be done.
3.  It was impossible to change the default significance level of
     0.05 for highlighting significant genetic distances in output file.
4.  Missing data identifier other than "?" was not accepted.
5.  If a a project file (or the path to it) contained the letters "arb",
     then it was erroneously considered as a Batch file.
6.  Reported confidence interval around FST were badly reported by the
     bootstrap procedure in case of a single group and no Individual
     Level taken into account.
7.  Estimation of haplotype frequencies from distance matrix was not
     performed when "Conventional FST" option was selected.
8.  Locus-by-locus AMOVA reported incorrect results for Genotypic data
     when individuals had missing data for only one of their gene copy
     at a given locus.
9.  Reported number of indels differed according to the weight given to
     indels in the Option panel. This bug did not affect AMOVA
     computations.
10. For sequence data, a mixture of N's and missing data led to problems
     in identifying distinct DNA sequences from distance matrix, leading
     to slightly incorrect FST computations.
11. Exact test of population differentiation could not be performed when
     gametic phase was unknown. Now, this option has been restored, like
     in ver. 2.
12. Arlequin hanged when a given population was entered several times in
     the definition of group for the computation of genetic structure.
     Now, the error is simply flagged but the program does not hang.
13. For frequency data, it was impossible to use a predefined distance
     matrix.
14. Beta approximation of the significance of Tajima's D gave
     wrong results. This approximation has been suppressed and now we
     only report the significance level obtained from coalescent
15. Bad computation of inbreeding coefficients under the locus-by-locus
     AMOVA approach for genotypic data when phenotype frequencies were
     larger than one. The bug caused an overestimation of the local (FIS)
     and total (FIT) inbreeding level. For samples where phenotype
     frequencies were all set to 1, the inbreeding coefficients were
     correctly estimated.
16. Expected heterozygosity reported under HWE exact test section was
     inaccurately computed. This inaccuracy however did not affect the
     results of the HWE exact test, which does not use information on
     observed and expected heterozygosity.

-- 
Laurent Excoffier
Computational and Molecular Population Genetics (CMPG)
Zoological Institute, University of Bern
6, Baltzerstrasse, CH-3012 Bern, Switzerland
Tel: +41 31 631 30 31  Fax: +41 31 631 48 88
Email: laurent.excoffier at zoo.unibe.ch
URL: http://cmpg.unibe.ch/people/excoffier.htm

Laurent <laurent.excoffier at zoo.unibe.ch>