====== MSA ====== **[[http://i122server.vu-wien.ac.at/MSA/info.html/MSA_info.html|MSA]]**\\ \\ Version 4.05\\ The MSA software tool was designed to handle large microsatellite data sets. Microsatellite analyzer calculates the standard suit of descriptive statistics and provides input files for other software packages. ===== Program information ===== * platform independent ===== Data type handled ===== * Microsat ===== Input Files ===== * MSA can converts your data into following formats: * [[GENEPOP]] two digit format * [[MSVAR]] (Beaumont) input format for each population separately * [[STRUCTURE]] * [[ARLEQUIN]] * [[MIGRATE]] * [[IM]]-format \\ * Input files can be generated using spreadsheet software, such as Excel, in which the data are arranged either in one column per locus or two columns per locus (sample input file). If Excel is used to generate a MSA inputfile it has to be saved as "TAB DELIMITED" file. * As MSA was mainly designed for microsatellites, data should be entered as the PCR product size * Missing data: indicated by either an empty cell or a negative value, but do not enter ‘0’ as this would be treated as a PCR product of zero bases \\ * To modify the spread sheet insert 3 rows above and 3 columns to the right of your data * cell A1: whether your data are arranged in the one column (1) or two column (2) format * first column: * name of the population * take care that no cell remains empty, as MSA stops reading the data after the first empty cell. * second column: * specifies whether your data are inbred (h) or outbred (d) * the same allele needs to be entered twice when only a single allele was detected (empty cells are thought to be missing data) * Please note that this column must not remain empty * third column: * allows to group populations and some analyses will be also performed for the specified groups * Please note that this column must not remain empty * In the absence of grouping give the same number to all populations * only consecutive group numbers are allowed, but groups assigned without any constraints in order * first two rows: * information about each locus * first row specifies the repeat type (1, 2, 3, etc) * second row indicates the length of the sequence flanking the microsatellite (in bp) * In the case no information is provided in the second row (empty cell), MSA does not calculate the variance in repeat number, but the inferred repeat type is specified in the output file * This option allows MSA to calculate the number of repeats from your PCR product size * third row: * the name of the microsatellite locus * In the two-column format, MSA allows two different names for the same locus (each entered in one cell) \\ * Remarks: * For compatibility with PHYLIP the population labels are limited to 8 characters * For individual based distances, only the first 4 characters of the population label are used to label individuals. Therefore, it is highly advised that the first 4 characters differ among population labels. ==== example ==== 2 2 2 2 2 3 113 81 112 159 116 1770 X13444 1818 X65444 1774 X66788 1772 X65644 1792 X976545 Pop1 d 1 140 140 147 159 152 155 Pop1 d 1 134 134 147 151 184 186 Pop1 d 1 134 134 104 106 147 147 186 178 152 155 Pop2 d 1 134 136 104 100 159 153 186 172 152 155 Pop2 d 1 134 140 104 104 151 143 184 178 152 155 Pop2 d 1 134 134 104 104 147 151 186 188 152 152 Pop2 d 1 134 134 147 141 184 178 152 152 Pop3 h 2 104 104 Pop3 h 2 134 134 104 104 149 149 186 178 152 152 Pop3 d 2 134 134 147 147 184 186 152 155 Pop3 h 2 104 98 Pop3 d 2 104 106 186 178 155 155 ===== How to cite ===== * Dieringer, Daniel & Schlštterer, Christian (2003) Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes 3 (1), 167-169