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| Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
|---|---|---|---|---|
| 4 | 7 | 6 | 0.969 | test_plus |
| Clone Abstraction | Parameter Bindings |
| Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
|---|---|---|---|
| 1 | 4 | 453 | Bio/Emboss/Applications.py |
| 2 | 4 | 476 | Bio/Emboss/Applications.py |
| 3 | 4 | 507 | Bio/Emboss/Applications.py |
| 4 | 4 | 547 | Bio/Emboss/Applications.py |
| 5 | 4 | 591 | Bio/Emboss/Applications.py |
| 6 | 4 | 626 | Bio/Emboss/Applications.py |
| 7 | 4 | 665 | Bio/Emboss/Applications.py |
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_Option(["-intreefile","intreefile"],["input"],None,1,"tree file to score (phylip)"),_Option(["-dtype","dtype"],["input"],None,0,"distance type ([S]ymetric, [b]ranch score)") |
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_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") |
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_Option(["-sequence","sequence"],["input"],None,1,"seq file to sample (phylip)"),_Option(["-categories","catergories"],["input"],None,0,"file of input categories") |
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_Option(["-sequence","sequence"],["input"],None,1,"seq file to use (phylip)"),_Option(["-intreefile","intreefile"],["input"],None,0,"Phylip tree file") |
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_Option(["-sequence","sequence"],["input"],None,1,"seq file to use (phylip)"),_Option(["-intreefile","intreefile"],["input"],None,0,"Phylip tree file to score") |
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_Option(["-sequence","sequence"],["input"],None,1,"seq file to use (phylip)"),_Option(["-ncategories","ncategories"],["input"],None,0,"number of rate catergories (1-9)") |
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_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]") |
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_Option([ [[#variable71a128a0]], [[#variable71a12840]]],["input"],None,1, [[#variable71a12780]]),_Option([ [[#variable71a12720]], [[#variable71a126c0]]],["input"],None,0, [[#variable71a125e0]]) |
| CloneAbstraction |
| Parameter Index | Clone Instance | Parameter Name | Value |
|---|---|---|---|
| 1 | 1 | [[#71a128a0]] | "-intreefile" |
| 1 | 2 | [[#71a128a0]] | "-datafile" |
| 1 | 3 | [[#71a128a0]] | "-sequence" |
| 1 | 4 | [[#71a128a0]] | "-sequence" |
| 1 | 5 | [[#71a128a0]] | "-sequence" |
| 1 | 6 | [[#71a128a0]] | "-intreefile" |
| 1 | 7 | [[#71a128a0]] | "-sequence" |
| 2 | 1 | [[#71a12840]] | "intreefile" |
| 2 | 2 | [[#71a12840]] | "datafile" |
| 2 | 3 | [[#71a12840]] | "sequence" |
| 2 | 4 | [[#71a12840]] | "sequence" |
| 2 | 5 | [[#71a12840]] | "sequence" |
| 2 | 6 | [[#71a12840]] | "intreefile" |
| 2 | 7 | [[#71a12840]] | "sequence" |
| 3 | 1 | [[#71a12780]] | "tree file to score (phylip)" |
| 3 | 2 | [[#71a12780]] | "dist file to use (phylip)" |
| 3 | 3 | [[#71a12780]] | "seq file to sample (phylip)" |
| 3 | 4 | [[#71a12780]] | "seq file to use (phylip)" |
| 3 | 5 | [[#71a12780]] | "seq file to use (phylip)" |
| 3 | 6 | [[#71a12780]] | "file with phylip trees to make consensus from" |
| 3 | 7 | [[#71a12780]] | "seq file to use (phylip)" |
| 4 | 1 | [[#71a12720]] | "-dtype" |
| 4 | 2 | [[#71a12720]] | "-matrixtype" |
| 4 | 3 | [[#71a12720]] | "-categories" |
| 4 | 4 | [[#71a12720]] | "-intreefile" |
| 4 | 5 | [[#71a12720]] | "-intreefile" |
| 4 | 6 | [[#71a12720]] | "-method" |
| 4 | 7 | [[#71a12720]] | "-ncategories" |
| 5 | 1 | [[#71a126c0]] | "dtype" |
| 5 | 2 | [[#71a126c0]] | "matrixtype" |
| 5 | 3 | [[#71a126c0]] | "catergories" |
| 5 | 4 | [[#71a126c0]] | "intreefile" |
| 5 | 5 | [[#71a126c0]] | "intreefile" |
| 5 | 6 | [[#71a126c0]] | "method" |
| 5 | 7 | [[#71a126c0]] | "ncategories" |
| 6 | 1 | [[#71a125e0]] | "distance type ([S]ymetric, [b]ranch score)" |
| 6 | 2 | [[#71a125e0]] | "is martrix [S]quare pr [u]pper or [l]ower" |
| 6 | 3 | [[#71a125e0]] | "file of input categories" |
| 6 | 4 | [[#71a125e0]] | "Phylip tree file" |
| 6 | 5 | [[#71a125e0]] | "Phylip tree file to score" |
| 6 | 6 | [[#71a125e0]] | "consensus method [s, mr, MRE, ml]" |
| 6 | 7 | [[#71a125e0]] | "number of rate catergories (1-9)" |