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1 #Lines starting with hash (#) are ignored
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2 #Tool commands. Define full paths if needed. By default (not specified) means locations relative to .jar file in Hammock/dist foltder
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3 #clustalOmegaCommand=
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4 #hmmbuildCommand=
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5 #hmmsearchCommand=
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6 #hhmakeCommand=
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7 #hhsearchCommand=
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8 #reformatCommand=
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9 #Directory for all temporal files. Define full path if needed. Default (not specified): /tmp
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10 #tempDirectory=
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11 #Temporal files subdirectories. Define full paths if needed. Default (not specified): directories in tempDirectory/Hammock_temp/[time]/
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12 #fastaDirectory=
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13 #msaDirectory=
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14 #hmmDirectory=
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15 #hhDirectory=
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16 #hmmsearchOutDirectory=
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17 #hhalignOutDirectory=
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18 #hhsearchOutDirectory=
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19 #fastaDatabaseFile=
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20 #Tool parameters. Generally, it is not recommended to change this section.
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21 clustalOmegaParameters=
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22 hmmbuildParameters=--enone --fragthresh 1.0 --hand --wnone --amino
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23 hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 --nonull2
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24 hmmalignParameters=--outformat selex --amino
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25 hhmakeParameters=-M a2m -id 100 -diff inf -pcm 3 -nocontxt -v 0
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26 hhsearchParameters=-norealign -alt 1 -corr 0 -shift 0 -ssm 0 -tags -nocons -nopred -nodssp -sc 0 -v 0 -z 2 -Z 500000 -local -p 0.0 -vit -b 100.0 -E 100.0 -e 100.0 -z 100 -BLOSUM65
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