CloneSet44


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Clone
Mass
Clones in
CloneSet
Parameter
Count
Clone
Similarity
Syntax Category
[Sequence Length]
4760.969test_plus
Clone AbstractionParameter Bindings
Clone Instance
(Click to see clone)
Line CountSource Line
Source File
14453
Bio/Emboss/Applications.py
24476
Bio/Emboss/Applications.py
34507
Bio/Emboss/Applications.py
44547
Bio/Emboss/Applications.py
54591
Bio/Emboss/Applications.py
64626
Bio/Emboss/Applications.py
74665
Bio/Emboss/Applications.py
Clone Instance
1
Line Count
4
Source Line
453
Source File
Bio/Emboss/Applications.py

         _Option(["-intreefile","intreefile"],["input"],None,1,"tree file to score (phylip)"),_Option(["-dtype","dtype"],["input"],None,0,"distance type ([S]ymetric, [b]ranch score)")


Clone Instance
2
Line Count
4
Source Line
476
Source File
Bio/Emboss/Applications.py

         _Option(["-datafile","datafile"],["input"],None,1,"dist file to use (phylip)"),_Option(["-matrixtype","matrixtype"],["input"],None,0,"is martrix [S]quare pr [u]pper or [l]ower")


Clone Instance
3
Line Count
4
Source Line
507
Source File
Bio/Emboss/Applications.py

         _Option(["-sequence","sequence"],["input"],None,1,"seq file to sample (phylip)"),_Option(["-categories","catergories"],["input"],None,0,"file of input categories")


Clone Instance
4
Line Count
4
Source Line
547
Source File
Bio/Emboss/Applications.py

         _Option(["-sequence","sequence"],["input"],None,1,"seq file to use (phylip)"),_Option(["-intreefile","intreefile"],["input"],None,0,"Phylip tree file")


Clone Instance
5
Line Count
4
Source Line
591
Source File
Bio/Emboss/Applications.py

         _Option(["-sequence","sequence"],["input"],None,1,"seq file to use (phylip)"),_Option(["-intreefile","intreefile"],["input"],None,0,"Phylip tree file to score")


Clone Instance
6
Line Count
4
Source Line
626
Source File
Bio/Emboss/Applications.py

         _Option(["-sequence","sequence"],["input"],None,1,"seq file to use (phylip)"),_Option(["-ncategories","ncategories"],["input"],None,0,"number of rate catergories (1-9)")


Clone Instance
7
Line Count
4
Source Line
665
Source File
Bio/Emboss/Applications.py

         _Option(["-intreefile","intreefile"],["input"],None,1,"file with phylip trees to make consensus from"),_Option(["-method","method"],["input"],None,0,"consensus method [s, mr, MRE, ml]")


Clone AbstractionParameter Count: 6Parameter Bindings

_Option([ [[#variable71a128a0]], [[#variable71a12840]]],["input"],None,1, [[#variable71a12780]]),_Option([ [[#variable71a12720]], [[#variable71a126c0]]],["input"],None,0, [[#variable71a125e0]])
 

CloneAbstraction
Parameter Bindings
Parameter
Index
Clone
Instance
Parameter
Name
Value
11[[#71a128a0]]
"-intreefile" 
12[[#71a128a0]]
"-datafile" 
13[[#71a128a0]]
"-sequence" 
14[[#71a128a0]]
"-sequence" 
15[[#71a128a0]]
"-sequence" 
16[[#71a128a0]]
"-intreefile" 
17[[#71a128a0]]
"-sequence" 
21[[#71a12840]]
"intreefile" 
22[[#71a12840]]
"datafile" 
23[[#71a12840]]
"sequence" 
24[[#71a12840]]
"sequence" 
25[[#71a12840]]
"sequence" 
26[[#71a12840]]
"intreefile" 
27[[#71a12840]]
"sequence" 
31[[#71a12780]]
"tree file to score (phylip)" 
32[[#71a12780]]
"dist file to use (phylip)" 
33[[#71a12780]]
"seq file to sample (phylip)" 
34[[#71a12780]]
"seq file to use (phylip)" 
35[[#71a12780]]
"seq file to use (phylip)" 
36[[#71a12780]]
"file with phylip trees to make consensus from" 
37[[#71a12780]]
"seq file to use (phylip)" 
41[[#71a12720]]
"-dtype" 
42[[#71a12720]]
"-matrixtype" 
43[[#71a12720]]
"-categories" 
44[[#71a12720]]
"-intreefile" 
45[[#71a12720]]
"-intreefile" 
46[[#71a12720]]
"-method" 
47[[#71a12720]]
"-ncategories" 
51[[#71a126c0]]
"dtype" 
52[[#71a126c0]]
"matrixtype" 
53[[#71a126c0]]
"catergories" 
54[[#71a126c0]]
"intreefile" 
55[[#71a126c0]]
"intreefile" 
56[[#71a126c0]]
"method" 
57[[#71a126c0]]
"ncategories" 
61[[#71a125e0]]
"distance type ([S]ymetric, [b]ranch score)" 
62[[#71a125e0]]
"is martrix [S]quare pr [u]pper or [l]ower" 
63[[#71a125e0]]
"file of input categories" 
64[[#71a125e0]]
"Phylip tree file" 
65[[#71a125e0]]
"Phylip tree file to score" 
66[[#71a125e0]]
"consensus method [s, mr, MRE, ml]" 
67[[#71a125e0]]
"number of rate catergories (1-9)"