CloneSet24


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Clone
Mass
Clones in
CloneSet
Parameter
Count
Clone
Similarity
Syntax Category
[Sequence Length]
51650.958arguments
Clone AbstractionParameter Bindings
Clone Instance
(Click to see clone)
Line CountSource Line
Source File
1481
Bio/Align/Applications/_Mafft.py
2488
Bio/Align/Applications/_Mafft.py
3494
Bio/Align/Applications/_Mafft.py
44139
Bio/Align/Applications/_Mafft.py
54151
Bio/Align/Applications/_Mafft.py
64158
Bio/Align/Applications/_Mafft.py
74165
Bio/Align/Applications/_Mafft.py
84172
Bio/Align/Applications/_Mafft.py
94179
Bio/Align/Applications/_Mafft.py
104186
Bio/Align/Applications/_Mafft.py
115193
Bio/Align/Applications/_Mafft.py
125158
Bio/Align/Applications/_Muscle.py
135203
Bio/Align/Applications/_Muscle.py
14584
Bio/Align/Applications/_Prank.py
15590
Bio/Align/Applications/_Prank.py
165126
Bio/Align/Applications/_Prank.py
Clone Instance
1
Line Count
4
Source Line
81
Source File
Bio/Align/Applications/_Mafft.py

                    ["--weighti","weighti"],["input"],
                     lambda x:isinstance(x,types.FloatType),0,"Weighting factor for the consistency term calculated "+"from pairwise alignments. Default: 2.7"


Clone Instance
2
Line Count
4
Source Line
88
Source File
Bio/Align/Applications/_Mafft.py

                    ["--retree","retree"],["input"],
                     lambda x:isinstance(x,types.IntType),0,"Guide tree is built number times in the progressive "+"stage. Valid with 6mer distance. Default: 2"


Clone Instance
3
Line Count
4
Source Line
94
Source File
Bio/Align/Applications/_Mafft.py

                    ["--maxiterate","maxiterate"],["input"],
                     lambda x:isinstance(x,types.IntType),0,"Number cycles of iterative refinement are performed. "+"Default: 0"


Clone Instance
4
Line Count
4
Source Line
139
Source File
Bio/Align/Applications/_Mafft.py

                    ["--partsize","partsize"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"The number of partitions in the PartTree algorithm. "+"Default: 50"


Clone Instance
5
Line Count
4
Source Line
151
Source File
Bio/Align/Applications/_Mafft.py

                    ["--op","op"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Gap opening penalty at group-to-group alignment. "+"Default: 1.53"


Clone Instance
6
Line Count
4
Source Line
158
Source File
Bio/Align/Applications/_Mafft.py

                    ["--ep","ep"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Offset value, which works like gap extension penalty, "+"for group-to- group alignment. Default: 0.123"


Clone Instance
7
Line Count
4
Source Line
165
Source File
Bio/Align/Applications/_Mafft.py

                    ["--lop","lop"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Gap opening penalty at local pairwise alignment. "+"Default: 0.123"


Clone Instance
8
Line Count
4
Source Line
172
Source File
Bio/Align/Applications/_Mafft.py

                    ["--lep","lep"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Offset value at local pairwise alignment. "+"Default: 0.1"


Clone Instance
9
Line Count
4
Source Line
179
Source File
Bio/Align/Applications/_Mafft.py

                    ["--lexp","lexp"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Gap extension penalty at local pairwise alignment. "+"Default: -0.1"


Clone Instance
10
Line Count
4
Source Line
186
Source File
Bio/Align/Applications/_Mafft.py

                    ["--LOP","LOP"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Gap opening penalty to skip the alignment. "+"Default: -6.00"


Clone Instance
11
Line Count
5
Source Line
193
Source File
Bio/Align/Applications/_Mafft.py

                    ["--LEXP","LEXP"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Gap extension penalty to skip the alignment. "+"Default: 0.00"


Clone Instance
12
Line Count
5
Source Line
158
Source File
Bio/Align/Applications/_Muscle.py

                    ["-maxdiagbreak","maxdiagbreak"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Maximum distance between two diagonals that allows "+"them to merge into one diagonal"


Clone Instance
13
Line Count
5
Source Line
203
Source File
Bio/Align/Applications/_Muscle.py

                    ["-minsmoothscore","minsmoothscore"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Minimum smoothed score a column must have to "+"be an anchor"


Clone Instance
14
Line Count
5
Source Line
84
Source File
Bio/Align/Applications/_Prank.py

                    ["-gapext","gapext"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Gap extension probability. Default: dna 0.5 "+"/ prot 0.5"


Clone Instance
15
Line Count
5
Source Line
90
Source File
Bio/Align/Applications/_Prank.py

                    ["-dnafreqs","dnafreqs"],["input"],
                    lambda x:isinstance(x,types.StringType),0,"DNA frequencies - 'A,C,G,T'. eg '25,25,25,25' as a quote "+"surrounded string value. Default: empirical"


Clone Instance
16
Line Count
5
Source Line
126
Source File
Bio/Align/Applications/_Prank.py

                    ["-pwdist","pwdist"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Expected pairwise distance for computing guidetree. "+"Default: dna 0.25 / prot 0.5"


Clone AbstractionParameter Count: 5Parameter Bindings

[ [[#variable5d006ec0]], [[#variable5d006e60]]],["input"], lambda x:isinstance(x,types. [[#variable5d006d20]]),0, [[#variable5d006e00]]+ [[#variable5d006d40]]
 

CloneAbstraction
Parameter Bindings
Parameter
Index
Clone
Instance
Parameter
Name
Value
11[[#5d006ec0]]
"--LEXP" 
12[[#5d006ec0]]
"--LOP" 
13[[#5d006ec0]]
"--lexp" 
14[[#5d006ec0]]
"--lep" 
15[[#5d006ec0]]
"--lop" 
16[[#5d006ec0]]
"--ep" 
17[[#5d006ec0]]
"--op" 
18[[#5d006ec0]]
"--partsize" 
19[[#5d006ec0]]
"--maxiterate" 
110[[#5d006ec0]]
"--retree" 
111[[#5d006ec0]]
"--weighti" 
112[[#5d006ec0]]
"-minsmoothscore" 
113[[#5d006ec0]]
"-maxdiagbreak" 
114[[#5d006ec0]]
"-pwdist" 
115[[#5d006ec0]]
"-dnafreqs" 
116[[#5d006ec0]]
"-gapext" 
21[[#5d006e60]]
"LEXP" 
22[[#5d006e60]]
"LOP" 
23[[#5d006e60]]
"lexp" 
24[[#5d006e60]]
"lep" 
25[[#5d006e60]]
"lop" 
26[[#5d006e60]]
"ep" 
27[[#5d006e60]]
"op" 
28[[#5d006e60]]
"partsize" 
29[[#5d006e60]]
"maxiterate" 
210[[#5d006e60]]
"retree" 
211[[#5d006e60]]
"weighti" 
212[[#5d006e60]]
"minsmoothscore" 
213[[#5d006e60]]
"maxdiagbreak" 
214[[#5d006e60]]
"pwdist" 
215[[#5d006e60]]
"dnafreqs" 
216[[#5d006e60]]
"gapext" 
31[[#5d006d20]]
FloatType 
32[[#5d006d20]]
FloatType 
33[[#5d006d20]]
FloatType 
34[[#5d006d20]]
FloatType 
35[[#5d006d20]]
FloatType 
36[[#5d006d20]]
FloatType 
37[[#5d006d20]]
FloatType 
38[[#5d006d20]]
IntType 
39[[#5d006d20]]
IntType 
310[[#5d006d20]]
IntType 
311[[#5d006d20]]
FloatType 
312[[#5d006d20]]
FloatType 
313[[#5d006d20]]
IntType 
314[[#5d006d20]]
FloatType 
315[[#5d006d20]]
StringType 
316[[#5d006d20]]
FloatType 
41[[#5d006e00]]
"Gap extension penalty to skip the alignment. " 
42[[#5d006e00]]
"Gap opening penalty to skip the alignment. " 
43[[#5d006e00]]
"Gap extension penalty at local pairwise alignment. " 
44[[#5d006e00]]
"Offset value at local pairwise alignment. " 
45[[#5d006e00]]
"Gap opening penalty at local pairwise alignment. " 
46[[#5d006e00]]
"Offset value, which works like gap extension penalty, " 
47[[#5d006e00]]
"Gap opening penalty at group-to-group alignment. " 
48[[#5d006e00]]
"The number of partitions in the PartTree algorithm. " 
49[[#5d006e00]]
"Number cycles of iterative refinement are performed. " 
410[[#5d006e00]]
"Guide tree is built number times in the progressive " 
411[[#5d006e00]]
"Weighting factor for the consistency term calculated " 
412[[#5d006e00]]
"Minimum smoothed score a column must have to " 
413[[#5d006e00]]
"Maximum distance between two diagonals that allows " 
414[[#5d006e00]]
"Expected pairwise distance for computing guidetree. " 
415[[#5d006e00]]
"DNA frequencies - 'A,C,G,T'. eg '25,25,25,25' as a quote " 
416[[#5d006e00]]
"Gap extension probability. Default: dna 0.5 " 
51[[#5d006d40]]
"Default: 0.00" 
52[[#5d006d40]]
"Default: -6.00" 
53[[#5d006d40]]
"Default: -0.1" 
54[[#5d006d40]]
"Default: 0.1" 
55[[#5d006d40]]
"Default: 0.123" 
56[[#5d006d40]]
"for group-to- group alignment. Default: 0.123" 
57[[#5d006d40]]
"Default: 1.53" 
58[[#5d006d40]]
"Default: 50" 
59[[#5d006d40]]
"Default: 0" 
510[[#5d006d40]]
"stage. Valid with 6mer distance. Default: 2" 
511[[#5d006d40]]
"from pairwise alignments. Default: 2.7" 
512[[#5d006d40]]
"be an anchor" 
513[[#5d006d40]]
"them to merge into one diagonal" 
514[[#5d006d40]]
"Default: dna 0.25 / prot 0.5" 
515[[#5d006d40]]
"surrounded string value. Default: empirical" 
516[[#5d006d40]]
"/ prot 0.5"