CloneSet33


Clone Mass	Clones in CloneSet	Parameter Count	Clone Similarity	Syntax Category [Sequence Length]
3	14	5	0.957	or_test

Clone Abstraction

Parameter Bindings


Bio/Align/Applications/_Muscle.py
Bio/Align/Applications/_Muscle.py
Bio/Align/Applications/_Muscle.py
Bio/Align/Applications/_Muscle.py
Bio/Align/Applications/_Muscle.py
Bio/Blast/Applications.py
Bio/Blast/Applications.py
Bio/Blast/Applications.py
Bio/Blast/Applications.py
Bio/Blast/Applications.py
Bio/Blast/Applications.py
Bio/Blast/Applications.py
Bio/Sequencing/Applications/_Novoalign.py
Bio/Sequencing/Applications/_Novoalign.py

Clone Instance (Click to see clone)	Line Count	Source Line	Source File
1	3	41	Bio/Align/Applications/_Muscle.py
2	4	48	Bio/Align/Applications/_Muscle.py
3	4	52	Bio/Align/Applications/_Muscle.py
4	4	143	Bio/Align/Applications/_Muscle.py
5	4	149	Bio/Align/Applications/_Muscle.py
6	2	60	Bio/Blast/Applications.py
7	2	195	Bio/Blast/Applications.py
8	2	197	Bio/Blast/Applications.py
9	2	199	Bio/Blast/Applications.py
10	2	201	Bio/Blast/Applications.py
11	2	203	Bio/Blast/Applications.py
12	2	239	Bio/Blast/Applications.py
13	3	22	Bio/Sequencing/Applications/_Novoalign.py
14	3	25	Bio/Sequencing/Applications/_Novoalign.py

Clone Instance
1

Line Count
3

Source Line
41

Source File

Bio/Align/Applications/_Muscle.py

            _Option(["-out","out"],["output","file"],None,0,"Output filename",0)

Clone Instance
2

Line Count
4

Source Line
48

Source File

Bio/Align/Applications/_Muscle.py

            _Option(["-in1","in1"],["input","file"],None,0,"First input filename for profile alignment",0)

Clone Instance
3

Line Count
4

Source Line
52

Source File

Bio/Align/Applications/_Muscle.py

            _Option(["-in2","in2"],["input","file"],None,0,"Second input filename for a profile alignment",0)

Clone Instance
4

Line Count
4

Source Line
143

Source File

Bio/Align/Applications/_Muscle.py

            #log             File name            None.              Log file name (delete
            #                                                        existing file).
            _Option(["-log","log"],["output","file"],None,0,"Log file name",0)

Clone Instance
5

Line Count
4

Source Line
149

Source File

Bio/Align/Applications/_Muscle.py

            #loga            File name            None.              Log file name (append
            #                                                        to existing file).
            _Option(["-loga","loga"],["output","file"],None,0,"Log file name (append to existing file)",0)

Clone Instance
6

Line Count
2

Source Line
60

Source File

Bio/Blast/Applications.py

           _Option(["-O","seqalign_file"],["output","file"],None,0,"seqalign file to output.",False)

Clone Instance
7

Line Count
2

Source Line
195

Source File

Bio/Blast/Applications.py

           _Option(["-C","checkpoint_outfile"],["output","file"],None,0,"Output file for PSI-BLAST checkpointing.",False)

Clone Instance
8

Line Count
2

Source Line
197

Source File

Bio/Blast/Applications.py

           _Option(["-R","restart_infile"],["input","file"],None,0,"Input file for PSI-BLAST restart.",False)

Clone Instance
9

Line Count
2

Source Line
199

Source File

Bio/Blast/Applications.py

           _Option(["-k","hit_infile"],["input","file"],None,0,"Hit file for PHI-BLAST.",False)

Clone Instance
10

Line Count
2

Source Line
201

Source File

Bio/Blast/Applications.py

           _Option(["-Q","matrix_outfile"],["output","file"],None,0,"Output file for PSI-BLAST matrix in ASCII.",False)

Clone Instance
11

Line Count
2

Source Line
203

Source File

Bio/Blast/Applications.py

           _Option(["-B","align_infile"],["input","file"],None,0,"Input alignment file for PSI-BLAST restart.",False)

Clone Instance
12

Line Count
2

Source Line
239

Source File

Bio/Blast/Applications.py

           _Option(["-l","logfile"],["output","file"],None,0,"Logfile name.",False)

Clone Instance
13

Line Count
3

Source Line
22

Source File

Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-d","database"],["input","file"],None,0,"database filename",0)

Clone Instance
14

Line Count
3

Source Line
25

Source File

Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-f","readfile"],["input","file"],None,0,"read file",0)

Clone Abstraction

Parameter Count: 5

Parameter Bindings

#log             File name            None.              Log file name (delete
#                                                        existing file).
#loga            File name            None.              Log file name (append
#                                                        to existing file).
_Option([ [[#variable71a585e0]], [[#variable71a58560]]],[ [[#variable71a58500]],"file"],None,0, [[#variable71a58480]], [[#variable71a583e0]])

CloneAbstraction

Parameter Bindings
Parameter Index	Clone Instance	Parameter Name	Value
1	1	`[[#71a585e0]]`	"-d"
1	2	`[[#71a585e0]]`	"-f"
1	3	`[[#71a585e0]]`	"-O"
1	4	`[[#71a585e0]]`	"-C"
1	5	`[[#71a585e0]]`	"-R"
1	6	`[[#71a585e0]]`	"-k"
1	7	`[[#71a585e0]]`	"-Q"
1	8	`[[#71a585e0]]`	"-B"
1	9	`[[#71a585e0]]`	"-l"
1	10	`[[#71a585e0]]`	"-out"
1	11	`[[#71a585e0]]`	"-in1"
1	12	`[[#71a585e0]]`	"-in2"
1	13	`[[#71a585e0]]`	"-log"
1	14	`[[#71a585e0]]`	"-loga"
2	1	`[[#71a58560]]`	"database"
2	2	`[[#71a58560]]`	"readfile"
2	3	`[[#71a58560]]`	"seqalign_file"
2	4	`[[#71a58560]]`	"checkpoint_outfile"
2	5	`[[#71a58560]]`	"restart_infile"
2	6	`[[#71a58560]]`	"hit_infile"
2	7	`[[#71a58560]]`	"matrix_outfile"
2	8	`[[#71a58560]]`	"align_infile"
2	9	`[[#71a58560]]`	"logfile"
2	10	`[[#71a58560]]`	"out"
2	11	`[[#71a58560]]`	"in1"
2	12	`[[#71a58560]]`	"in2"
2	13	`[[#71a58560]]`	"log"
2	14	`[[#71a58560]]`	"loga"
3	1	`[[#71a58500]]`	"input"
3	2	`[[#71a58500]]`	"input"
3	3	`[[#71a58500]]`	"output"
3	4	`[[#71a58500]]`	"output"
3	5	`[[#71a58500]]`	"input"
3	6	`[[#71a58500]]`	"input"
3	7	`[[#71a58500]]`	"output"
3	8	`[[#71a58500]]`	"input"
3	9	`[[#71a58500]]`	"output"
3	10	`[[#71a58500]]`	"output"
3	11	`[[#71a58500]]`	"input"
3	12	`[[#71a58500]]`	"input"
3	13	`[[#71a58500]]`	"output"
3	14	`[[#71a58500]]`	"output"
4	1	`[[#71a58480]]`	"database filename"
4	2	`[[#71a58480]]`	"read file"
4	3	`[[#71a58480]]`	"seqalign file to output."
4	4	`[[#71a58480]]`	"Output file for PSI-BLAST checkpointing."
4	5	`[[#71a58480]]`	"Input file for PSI-BLAST restart."
4	6	`[[#71a58480]]`	"Hit file for PHI-BLAST."
4	7	`[[#71a58480]]`	"Output file for PSI-BLAST matrix in ASCII."
4	8	`[[#71a58480]]`	"Input alignment file for PSI-BLAST restart."
4	9	`[[#71a58480]]`	"Logfile name."
4	10	`[[#71a58480]]`	"Output filename"
4	11	`[[#71a58480]]`	"First input filename for profile alignment"
4	12	`[[#71a58480]]`	"Second input filename for a profile alignment"
4	13	`[[#71a58480]]`	"Log file name"
4	14	`[[#71a58480]]`	"Log file name (append to existing file)"
5	1	`[[#71a583e0]]`	0
5	2	`[[#71a583e0]]`	0
5	3	`[[#71a583e0]]`	False
5	4	`[[#71a583e0]]`	False
5	5	`[[#71a583e0]]`	False
5	6	`[[#71a583e0]]`	False
5	7	`[[#71a583e0]]`	False
5	8	`[[#71a583e0]]`	False
5	9	`[[#71a583e0]]`	False
5	10	`[[#71a583e0]]`	0
5	11	`[[#71a583e0]]`	0
5	12	`[[#71a583e0]]`	0
5	13	`[[#71a583e0]]`	0
5	14	`[[#71a583e0]]`	0