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| Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
|---|---|---|---|---|
| 4 | 7 | 4 | 0.968 | or_test |
| Clone Abstraction | Parameter Bindings |
| Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
|---|---|---|---|
| 1 | 4 | 79 | Bio/Align/Applications/_Prank.py |
| 2 | 4 | 96 | Bio/Align/Applications/_Prank.py |
| 3 | 4 | 101 | Bio/Align/Applications/_Prank.py |
| 4 | 4 | 162 | Bio/Align/Applications/_Prank.py |
| 5 | 4 | 167 | Bio/Align/Applications/_Prank.py |
| 6 | 4 | 173 | Bio/Align/Applications/_Prank.py |
| 7 | 4 | 179 | Bio/Align/Applications/_Prank.py |
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#-gaprate=# [gap opening rate; default: dna 0.025 / prot 0.0025]
_Option(["-gaprate","gaprate"],["input"],
lambda x:isinstance(x,types.FloatType),0,"Gap opening rate. Default: dna 0.025 prot 0.0025")
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#-kappa=# [ts/tv rate ratio; default:2]
_Option(["-kappa","kappa"],["input"],
lambda x:isinstance(x,types.IntType),0,"Transition/transversion ratio. Default: 2")
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#-rho=# [pur/pyr rate ratio; default:1]
_Option(["-rho","rho"],["input"],
lambda x:isinstance(x,types.IntType),0,"Purine/pyrimidine ratio. Default: 1")
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#-pwgenomicdist=# [distance for pairwise alignment; default: 0.3]
_Option(["-pwgenomicdist","pwgenomicdist"],["input"],
lambda x:isinstance(x,types.FloatType),0,"Distance for pairwise alignment. Default: 0.3")
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#-scalebranches=# [scale branch lengths; default: dna 1 / prot 2]
_Option(["-scalebranches","scalebranches"],["input"],
lambda x:isinstance(x,types.IntType),0,"Scale branch lengths. Default: dna 1 / prot 2")
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#-fixedbranches=# [use fixed branch lengths]
#Assume looking for a float
_Option(["-fixedbranches","fixedbranches"],["input"],
lambda x:isinstance(x,types.FloatType),0,"Use fixed branch lengths of input value")
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#-maxbranches=# [set maximum branch length]
#Assume looking for a float
_Option(["-maxbranches","maxbranches"],["input"],
lambda x:isinstance(x,types.FloatType),0,"Use maximum branch lengths of input value")
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#-maxbranches=# [set maximum branch length] #-fixedbranches=# [use fixed branch lengths] #Assume looking for a float #-scalebranches=# [scale branch lengths; default: dna 1 / prot 2] #-pwgenomicdist=# [distance for pairwise alignment; default: 0.3] #-rho=# [pur/pyr rate ratio; default:1] #-kappa=# [ts/tv rate ratio; default:2] #-gaprate=# [gap opening rate; default: dna 0.025 / prot 0.0025] _Option([ [[#variable4fdb96c0]], [[#variable5f4b3d40]]],["input"], lambda x:isinstance(x,types. [[#variable4fdb95e0]]),0, [[#variable4fdb9640]]) |
| CloneAbstraction |
| Parameter Index | Clone Instance | Parameter Name | Value |
|---|---|---|---|
| 1 | 1 | [[#4fdb96c0]] | "-maxbranches" |
| 1 | 2 | [[#4fdb96c0]] | "-fixedbranches" |
| 1 | 3 | [[#4fdb96c0]] | "-scalebranches" |
| 1 | 4 | [[#4fdb96c0]] | "-pwgenomicdist" |
| 1 | 5 | [[#4fdb96c0]] | "-rho" |
| 1 | 6 | [[#4fdb96c0]] | "-kappa" |
| 1 | 7 | [[#4fdb96c0]] | "-gaprate" |
| 2 | 1 | [[#5f4b3d40]] | "maxbranches" |
| 2 | 2 | [[#5f4b3d40]] | "fixedbranches" |
| 2 | 3 | [[#5f4b3d40]] | "scalebranches" |
| 2 | 4 | [[#5f4b3d40]] | "pwgenomicdist" |
| 2 | 5 | [[#5f4b3d40]] | "rho" |
| 2 | 6 | [[#5f4b3d40]] | "kappa" |
| 2 | 7 | [[#5f4b3d40]] | "gaprate" |
| 3 | 1 | [[#4fdb95e0]] | FloatType |
| 3 | 2 | [[#4fdb95e0]] | FloatType |
| 3 | 3 | [[#4fdb95e0]] | IntType |
| 3 | 4 | [[#4fdb95e0]] | FloatType |
| 3 | 5 | [[#4fdb95e0]] | IntType |
| 3 | 6 | [[#4fdb95e0]] | IntType |
| 3 | 7 | [[#4fdb95e0]] | FloatType |
| 4 | 1 | [[#4fdb9640]] | "Use maximum branch lengths of input value" |
| 4 | 2 | [[#4fdb9640]] | "Use fixed branch lengths of input value" |
| 4 | 3 | [[#4fdb9640]] | "Scale branch lengths. Default: dna 1 / prot 2" |
| 4 | 4 | [[#4fdb9640]] | "Distance for pairwise alignment. Default: 0.3" |
| 4 | 5 | [[#4fdb9640]] | "Purine/pyrimidine ratio. Default: 1" |
| 4 | 6 | [[#4fdb9640]] | "Transition/transversion ratio. Default: 2" |
| 4 | 7 | [[#4fdb9640]] | "Gap opening rate. Default: dna 0.025 prot 0.0025" |