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