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author hammock
date Mon, 26 Jan 2015 06:24:21 -0500
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#Change "default" to full path if needed. Default means locations relative to .jar file in PhageClust/dist foltder
#clustalOmegaCommand=
#fastaDirectory=
#msaDirectory=
clustalOmegaParameters=--iter=5 --full-iter
hmmbuildParameters=--enone --fragthresh 1.0 --symfrac 0.6
hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2
hhmakeParameters=-M a2m -id 100 -qsc -100 -pcm 3
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
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
reformatParameters=-M 30