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Binary Matrix (01 matrix) - Data Export
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GelQuest offers several formats for exporting binary matrix data.
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Please note:
1. Only those hyperbins containing active bins, i.e. they were included
by the hyperbin detection parameters and they must not be disabled by
the user, are exported into an 01 matrix.
2. Only visible color channels will be exported.
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Format
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Example
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NEXUS
For use with the PAUP
software.
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#NEXUS
begin data;
dimensions ntax=3 nchar=10;
format datatype=standard [interleave] missing=?;
matrix
'Sample#1' 1111101111
'Sample#2' 0011110111
'Sample#3' 0111101111
;
END;
BEGIN PAUP;
[Calculate a simple UPGMA-Tree]
UPGMA BRLENS=yes BREAKTIES=random TIESEED=123
TREEFILE=upgma_tree REPLACE=yes;
[Do UPGMA-Bootstrapping]
set criterion=distance;
bootstrap NREPS=100 SEARCH=UPGMA
TREEFILE=upgma_boostrap.tre BRLENS=yes REPLACE=yes;
END;
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NEWICK
For use with PHYLIP and other
software.
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3 10
Sample#1 1111101111
Sample#2 0011110111
Sample#3 0111101111
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SIMPLE
For downstream processing
with other software.
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3
'Sample#1' 1111101111
'Sample#2' 0011110111
'Sample#3' 0111101111
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FASTA
For other software.
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>Sample#1
1111101111
>Sample#2
0011110111
>Sample#3
0111101111
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