HAPLOTYPE ANALYSIS is a new software for analysis of data from organelle genomes (chloroplast or mitochondrial) which are observed from microsatellites (SSR) or PCR-RFLP markers. The main advantage of this software is that the analysis is performed based on the frequency of haplotypes, which was identified by combining the size variants at the investigated microsatellites (SSR) loci or by combining the restricted fragments of PCR-RFLP loci. The analysis initiates by estimating haplotype frequencies in each population, and in continuation it calculates genetic diversity within each population (intra-population analysis) by
NOTE: For microsatellite markers (chloroplast, mitochondrial) the average genetic distances among the individuals within datasets were estimated using the value of Dsh2 (Goldstein et al., 1995), based on the average squared sum of all length differences at microsatellites and with the assumption of the stepwise mutation model (Morgante et al., 1998).
Population genetic structure from the population samples (inter-population analysis) is computed utilizing
HAPLOTYPE ANALYSIS v1.0b is a first test version of software written in Visual Basic for Applications (VBA) within Excel. On the PC, it is compatible with Excel 97 upwards under Windows 95, 98 and 2000, while it has been extensively tested and run in Excel 2002 and Excel 2003 under Windows XP. This first version is possible to contain bugs, some of which are probably easy to detect. However, the authors would appreciate to be informed of any detected bug; in which case please send a sample data file and type of software used, while any suggestions for improvement of the scope and/or of the functionality of the program are welcome (Email firstname.lastname@example.org and/or email@example.com)
Download software and User's Manual as the zipped file
Eliades N-G., Eliades D. G. (2009). HAPLOTYPE ANALYSIS: Software for analysis of haplotype data. Distributed by the authors. Forest Genetics and Forest Tree Breeding, Georg-August University Goettingen, Germany. URL http://www.uni-goettingen.de/en/134935.html
HAPLOTYPE ANALYSIS is free software: you can redistribute it under the terms of the GNU General Public License (GPL) v.3, as published by the Free Software Foundation. HAPLOTYPE ANALYSIS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of merchantability or fitness for a particular purpose. Reassembling is not permitted. See the GNU General Public License, a copy of which is contained in the file "gpl.txt" included in the download file, or see http://www.gnu.org/licenses/.