Welcome to Power Marker demonstration

Report
Welcome to Power Marker
demonstration
Md. Sazzadur Rahman
14 March 2012
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Installation:
Install first : Microsoft .NET framework redistributable (it can be getting free from
following link
(http://msdn.microsoft.com/library/default.asp?url=/downloads/list/netdevframework.asp)
Install Power marker: It’s free and can be download from
(http://www.powermarker.net)
Install Tree View for viewing tree or to install MEGA for tree view
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Data Format:
NTSys used qualitative data like presence/absence of allele
Genotype
g1
g2
g3
m1
0
1
0
0
0
1
1
0
0
But PM used quantitative data like actual allele size i.e. molecular weight of alleles
Genotype
g1
g2
g3
m1
122
145
130
m2
225
230
200
m3
330
340
380
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Measurement of allele size:
Allele size i.e. Molecular weight of each allele can be measured manually or by
using through Alpha Ease soft of Alpha Imager Gel documentation system
200 bp
100 bp
RM7075 (10% PAGE) with 1 kb+ ladder)
Manually measured molecular weight
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Format of input file:
5 different type format: Plain TXT, TABLE-like, FREQUENCY, DISTANCE FORMAT,
PHYLIP FORMAT
PLAIN TXT FORMAT
Prepare xls or xlsx file as sample file
Save the xls or xlsx file to text tab delimited file
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Preparing project and importing of data file
First prepare a folder in any desired location for storing Project and all result files
Click on the file menu and closing all projects
Click on the new for making a new projects with extension “.prj”
Click on the file menu again and then click on import then Dataset
A box will appear then click on “From text file” and select file (Text tab file
prepare before) location by Browse button
Check click on ‘TAB’ in Column Delimiter and ‘Customized Format’ on Table
Format then click on “NEXT”
Contd. Next page
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Continuation from previous page
Select genotype and click on categorical then click on drop down button Level-1
and select sample then click Next
Select ‘The dataset is genotype data and the gametic phase is unknown’ on data
type and change the missing numeric as -9/-9 and click Next
Click finish to complete data input
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Analysis-I (STAT)
Click Analysis on Menu bar, select Summary then clicking on Summary Statistics
Select ‘Input file format’ and write a folder name like ‘Summary stat’ on Result
Folder and Check/select checker boxes as per your analysis (If you want to see
your analysis on XL file then you can select ‘Open computed tables in Excel)
Click Submit (within second analysis will be done & result will appear)
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Analysis-II (UPGMA)
Click Analysis on menu bar and select Phylogeny then select on Compute frequency
A box will appear select ‘input file format’, write name like ‘Result Freq’ on Result Folder
and then click only in the checker box “Compute frequency on level-1” and then click on
Submit
Again go similar way as MENU BAR—ANALYSIS—PHYLOGENY—COMPUTE FREQUENCY
BASED DISTANCE
A box will appear select ‘input file format.frequency’, write name like ‘Result Freq Dist’ on
Result Folder and then click only in the checker box “SharedAllele” and then click on
Submit
Again go similar way as MENU BAR—ANALYSIS—PHYLOGENY—UPGMA/NJ Tree
A box will appear select ‘input file format.frequency.SharedAllele’, write name like ‘Result
Freq Dist SA’ on Result Folder and then click only in the checker box “UPGMA” ; View
result in Power Maker and Open Tree in Tree View and then click on Submit
Tree will appear in TREE VIEW OR in MEGA
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Thanks for your patience and cooperation
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