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annotate Hammock/settings/settings.prop~ @ 0:b1ac138f0287 draft

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author hammock
date Mon, 26 Jan 2015 06:24:21 -0500
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hammock
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1 #Change "default" to full path if needed. Default means locations relative to .jar file in PhageClust/dist foltder
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hammock
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2 #clustalOmegaCommand=
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hammock
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3 #fastaDirectory=
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hammock
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4 #msaDirectory=
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hammock
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5 clustalOmegaParameters=--iter=5 --full-iter
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hammock
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6 hmmbuildParameters=--enone --fragthresh 1.0 --symfrac 0.6
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hammock
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7 hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2
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hammock
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8 hhmakeParameters=-M a2m -id 100 -qsc -100 -pcm 3
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hammock
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9 hhalignParameters=-realign -id 100 -diff inf -alt 1 -corr 0 -shift 0 -ssm 0 -nocontxt -pcm 2 -tags -nocons -nopred -nodssp -M a2m -alt 1 -sc 0 -v 0 -z 2 -Z 20 -local -mact 0.0
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hammock
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10 hhsearchParameters=-realign -id 100 -diff inf -alt 1 -corr 0 -shift 0 -ssm 0 -nocontxt -pcm 2 -tags -nocons -nopred -nodssp -M a2m -alt 1 -sc 0 -v 0 -z 2 -Z 500 -local -mact 0.0 -p 0
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hammock
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11 reformatParameters=-M 30