Download Manual - Copycat

Contents
1 Checklist
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2 The first start
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3 Copycat - The first tab
3.1 Finding NCBI taxonomy IDs . . . . . . . . . . . . .
3.1.1 Characteristics of the association table . . . .
3.2 Computation of the broken-stick distribution (BSD)
solved associations . . . . . . . . . . . . . . . . . . .
3.3 Filtering of an association table . . . . . . . . . . . .
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4 Copycat - The second tab
4.1 Step 1 . . . . . . . . . . . . . . . . . . . . .
4.2 Step 2 . . . . . . . . . . . . . . . . . . . . .
4.3 Step 3 (create host distance matrix) . . . .
4.4 Step 4 (create the parasite distance matrix)
4.5 Step 5 (validation) . . . . . . . . . . . . . .
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5 Copycat - The third tab
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6 Copycat – Available menu bar options
6.1 File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.1.1 ”Transfer content of working directory to a place of your choice”
6.1.2 ”Download NCBI taxonomy file(s)” . . . . . . . . . . . . . . . .
6.2 View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.2.1 ”View content of working directory” . . . . . . . . . . . . . . . .
6.3 Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.3.1 ”Enable Strict Filtering of Association Table” . . . . . . . . . . .
6.3.2 ”Use Equal Branch Length (=1) for tree2dist Conversion” . . . .
6.3.3 ”Use AxPcoords and AxParafit instead of DistPCoA and Parafit”
6.4 Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.4.1 ”Show setup menu at next program start” . . . . . . . . . . . . .
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7 Tutorial - A step-by-step example run of Copycat
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