| Previous CloneSet | Next CloneSet | Back to Main Report |
| Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
|---|---|---|---|---|
| 5 | 16 | 5 | 0.958 | arguments |
| Clone Abstraction | Parameter Bindings |
| Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
|---|---|---|---|
| 1 | 4 | 81 | Bio/Align/Applications/_Mafft.py |
| 2 | 4 | 88 | Bio/Align/Applications/_Mafft.py |
| 3 | 4 | 94 | Bio/Align/Applications/_Mafft.py |
| 4 | 4 | 139 | Bio/Align/Applications/_Mafft.py |
| 5 | 4 | 151 | Bio/Align/Applications/_Mafft.py |
| 6 | 4 | 158 | Bio/Align/Applications/_Mafft.py |
| 7 | 4 | 165 | Bio/Align/Applications/_Mafft.py |
| 8 | 4 | 172 | Bio/Align/Applications/_Mafft.py |
| 9 | 4 | 179 | Bio/Align/Applications/_Mafft.py |
| 10 | 4 | 186 | Bio/Align/Applications/_Mafft.py |
| 11 | 5 | 193 | Bio/Align/Applications/_Mafft.py |
| 12 | 5 | 158 | Bio/Align/Applications/_Muscle.py |
| 13 | 5 | 203 | Bio/Align/Applications/_Muscle.py |
| 14 | 5 | 84 | Bio/Align/Applications/_Prank.py |
| 15 | 5 | 90 | Bio/Align/Applications/_Prank.py |
| 16 | 5 | 126 | Bio/Align/Applications/_Prank.py |
| ||||
["--weighti","weighti"],["input"],
lambda x:isinstance(x,types.FloatType),0,"Weighting factor for the consistency term calculated "+"from pairwise alignments. Default: 2.7"
|
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["--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"
|
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["--maxiterate","maxiterate"],["input"],
lambda x:isinstance(x,types.IntType),0,"Number cycles of iterative refinement are performed. "+"Default: 0"
|
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["--partsize","partsize"],["input"],
lambda x:isinstance(x,types.IntType),0,"The number of partitions in the PartTree algorithm. "+"Default: 50"
|
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["--op","op"],["input"],
lambda x:isinstance(x,types.FloatType),0,"Gap opening penalty at group-to-group alignment. "+"Default: 1.53"
|
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["--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"
|
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["--lop","lop"],["input"],
lambda x:isinstance(x,types.FloatType),0,"Gap opening penalty at local pairwise alignment. "+"Default: 0.123"
|
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["--lep","lep"],["input"],
lambda x:isinstance(x,types.FloatType),0,"Offset value at local pairwise alignment. "+"Default: 0.1"
|
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["--lexp","lexp"],["input"],
lambda x:isinstance(x,types.FloatType),0,"Gap extension penalty at local pairwise alignment. "+"Default: -0.1"
|
| ||||
["--LOP","LOP"],["input"],
lambda x:isinstance(x,types.FloatType),0,"Gap opening penalty to skip the alignment. "+"Default: -6.00"
|
| ||||
["--LEXP","LEXP"],["input"],
lambda x:isinstance(x,types.FloatType),0,"Gap extension penalty to skip the alignment. "+"Default: 0.00"
|
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["-maxdiagbreak","maxdiagbreak"],["input"],
lambda x:isinstance(x,types.IntType),0,"Maximum distance between two diagonals that allows "+"them to merge into one diagonal"
|
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["-minsmoothscore","minsmoothscore"],["input"],
lambda x:isinstance(x,types.FloatType),0,"Minimum smoothed score a column must have to "+"be an anchor"
|
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["-gapext","gapext"],["input"],
lambda x:isinstance(x,types.FloatType),0,"Gap extension probability. Default: dna 0.5 "+"/ prot 0.5"
|
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["-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"
|
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["-pwdist","pwdist"],["input"],
lambda x:isinstance(x,types.FloatType),0,"Expected pairwise distance for computing guidetree. "+"Default: dna 0.25 / prot 0.5"
|
| |||
[ [[#variable5d006ec0]], [[#variable5d006e60]]],["input"], lambda x:isinstance(x,types. [[#variable5d006d20]]),0, [[#variable5d006e00]]+ [[#variable5d006d40]] |
| CloneAbstraction |
| Parameter Index | Clone Instance | Parameter Name | Value |
|---|---|---|---|
| 1 | 1 | [[#5d006ec0]] | "--LEXP" |
| 1 | 2 | [[#5d006ec0]] | "--LOP" |
| 1 | 3 | [[#5d006ec0]] | "--lexp" |
| 1 | 4 | [[#5d006ec0]] | "--lep" |
| 1 | 5 | [[#5d006ec0]] | "--lop" |
| 1 | 6 | [[#5d006ec0]] | "--ep" |
| 1 | 7 | [[#5d006ec0]] | "--op" |
| 1 | 8 | [[#5d006ec0]] | "--partsize" |
| 1 | 9 | [[#5d006ec0]] | "--maxiterate" |
| 1 | 10 | [[#5d006ec0]] | "--retree" |
| 1 | 11 | [[#5d006ec0]] | "--weighti" |
| 1 | 12 | [[#5d006ec0]] | "-minsmoothscore" |
| 1 | 13 | [[#5d006ec0]] | "-maxdiagbreak" |
| 1 | 14 | [[#5d006ec0]] | "-pwdist" |
| 1 | 15 | [[#5d006ec0]] | "-dnafreqs" |
| 1 | 16 | [[#5d006ec0]] | "-gapext" |
| 2 | 1 | [[#5d006e60]] | "LEXP" |
| 2 | 2 | [[#5d006e60]] | "LOP" |
| 2 | 3 | [[#5d006e60]] | "lexp" |
| 2 | 4 | [[#5d006e60]] | "lep" |
| 2 | 5 | [[#5d006e60]] | "lop" |
| 2 | 6 | [[#5d006e60]] | "ep" |
| 2 | 7 | [[#5d006e60]] | "op" |
| 2 | 8 | [[#5d006e60]] | "partsize" |
| 2 | 9 | [[#5d006e60]] | "maxiterate" |
| 2 | 10 | [[#5d006e60]] | "retree" |
| 2 | 11 | [[#5d006e60]] | "weighti" |
| 2 | 12 | [[#5d006e60]] | "minsmoothscore" |
| 2 | 13 | [[#5d006e60]] | "maxdiagbreak" |
| 2 | 14 | [[#5d006e60]] | "pwdist" |
| 2 | 15 | [[#5d006e60]] | "dnafreqs" |
| 2 | 16 | [[#5d006e60]] | "gapext" |
| 3 | 1 | [[#5d006d20]] | FloatType |
| 3 | 2 | [[#5d006d20]] | FloatType |
| 3 | 3 | [[#5d006d20]] | FloatType |
| 3 | 4 | [[#5d006d20]] | FloatType |
| 3 | 5 | [[#5d006d20]] | FloatType |
| 3 | 6 | [[#5d006d20]] | FloatType |
| 3 | 7 | [[#5d006d20]] | FloatType |
| 3 | 8 | [[#5d006d20]] | IntType |
| 3 | 9 | [[#5d006d20]] | IntType |
| 3 | 10 | [[#5d006d20]] | IntType |
| 3 | 11 | [[#5d006d20]] | FloatType |
| 3 | 12 | [[#5d006d20]] | FloatType |
| 3 | 13 | [[#5d006d20]] | IntType |
| 3 | 14 | [[#5d006d20]] | FloatType |
| 3 | 15 | [[#5d006d20]] | StringType |
| 3 | 16 | [[#5d006d20]] | FloatType |
| 4 | 1 | [[#5d006e00]] | "Gap extension penalty to skip the alignment. " |
| 4 | 2 | [[#5d006e00]] | "Gap opening penalty to skip the alignment. " |
| 4 | 3 | [[#5d006e00]] | "Gap extension penalty at local pairwise alignment. " |
| 4 | 4 | [[#5d006e00]] | "Offset value at local pairwise alignment. " |
| 4 | 5 | [[#5d006e00]] | "Gap opening penalty at local pairwise alignment. " |
| 4 | 6 | [[#5d006e00]] | "Offset value, which works like gap extension penalty, " |
| 4 | 7 | [[#5d006e00]] | "Gap opening penalty at group-to-group alignment. " |
| 4 | 8 | [[#5d006e00]] | "The number of partitions in the PartTree algorithm. " |
| 4 | 9 | [[#5d006e00]] | "Number cycles of iterative refinement are performed. " |
| 4 | 10 | [[#5d006e00]] | "Guide tree is built number times in the progressive " |
| 4 | 11 | [[#5d006e00]] | "Weighting factor for the consistency term calculated " |
| 4 | 12 | [[#5d006e00]] | "Minimum smoothed score a column must have to " |
| 4 | 13 | [[#5d006e00]] | "Maximum distance between two diagonals that allows " |
| 4 | 14 | [[#5d006e00]] | "Expected pairwise distance for computing guidetree. " |
| 4 | 15 | [[#5d006e00]] | "DNA frequencies - 'A,C,G,T'. eg '25,25,25,25' as a quote " |
| 4 | 16 | [[#5d006e00]] | "Gap extension probability. Default: dna 0.5 " |
| 5 | 1 | [[#5d006d40]] | "Default: 0.00" |
| 5 | 2 | [[#5d006d40]] | "Default: -6.00" |
| 5 | 3 | [[#5d006d40]] | "Default: -0.1" |
| 5 | 4 | [[#5d006d40]] | "Default: 0.1" |
| 5 | 5 | [[#5d006d40]] | "Default: 0.123" |
| 5 | 6 | [[#5d006d40]] | "for group-to- group alignment. Default: 0.123" |
| 5 | 7 | [[#5d006d40]] | "Default: 1.53" |
| 5 | 8 | [[#5d006d40]] | "Default: 50" |
| 5 | 9 | [[#5d006d40]] | "Default: 0" |
| 5 | 10 | [[#5d006d40]] | "stage. Valid with 6mer distance. Default: 2" |
| 5 | 11 | [[#5d006d40]] | "from pairwise alignments. Default: 2.7" |
| 5 | 12 | [[#5d006d40]] | "be an anchor" |
| 5 | 13 | [[#5d006d40]] | "them to merge into one diagonal" |
| 5 | 14 | [[#5d006d40]] | "Default: dna 0.25 / prot 0.5" |
| 5 | 15 | [[#5d006d40]] | "surrounded string value. Default: empirical" |
| 5 | 16 | [[#5d006d40]] | "/ prot 0.5" |