Masterarbeit, Heidi Lischer

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====== MSA ======
**[[http://i122server.vu-wien.ac.at/MSA/info.html/MSA_info.html|MSA]]**\\

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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

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  * 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

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  * 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)

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  * 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 ====
<code>
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
</code>

===== 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