Skip to content

Instantly share code, notes, and snippets.

@Zsailer
Last active August 29, 2015 14:27
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save Zsailer/0cd1f110ae297ecaf79a to your computer and use it in GitHub Desktop.
Save Zsailer/0cd1f110ae297ecaf79a to your computer and use it in GitHub Desktop.
metadata
// Metadata for networks and trajectories from the following paper:
// "Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins"
// Weinreich, D., et.al
// http://www.sciencemag.org/content/312/5770/111.short
{
"directed": true,
"nodes": [
{
"value": 1.0152510120727598,
"binary": "00000",
"id": 0,
"genotype": "gAEMG",
"errors": null,
"phenotype": 1.0152510120727598
},
{
"errors": null,
"id": 1,
"phenotype": 1.0556310301916847,
"genotype": "gAEMS",
"binary": "00001",
"value": 1.0556310301916847
},
{
"errors": null,
"id": 2,
"phenotype": 1.0068622184069904,
"genotype": "gAETG",
"binary": "00010",
"value": 1.0068622184069904
},
{
"errors": null,
"id": 3,
"phenotype": 1.0248139196992883,
"genotype": "gAKMG",
"binary": "00100",
"value": 1.0248139196992883
},
{
"errors": null,
"id": 4,
"phenotype": 1.0152510120727598,
"genotype": "gGEMG",
"binary": "01000",
"value": 1.0152510120727598
},
{
"errors": null,
"id": 5,
"phenotype": 1.0152510120727598,
"genotype": "aAEMG",
"binary": "10000",
"value": 1.0152510120727598
},
{
"errors": null,
"id": 6,
"phenotype": 1.0931151178699843,
"genotype": "gAETS",
"binary": "00011",
"value": 1.0931151178699843
},
{
"errors": null,
"id": 7,
"phenotype": 1.113243817588169,
"genotype": "gAKMS",
"binary": "00101",
"value": 1.113243817588169
},
{
"errors": null,
"id": 8,
"phenotype": 1.0786314673865984,
"genotype": "gGEMS",
"binary": "01001",
"value": 1.0786314673865984
},
{
"errors": null,
"id": 9,
"phenotype": 1.0556310301916847,
"genotype": "aAEMS",
"binary": "10001",
"value": 1.0556310301916847
},
{
"errors": null,
"id": 10,
"phenotype": 1.0334809063896502,
"genotype": "gAKTG",
"binary": "00110",
"value": 1.0334809063896502
},
{
"errors": null,
"id": 11,
"phenotype": 1.0556310301916847,
"genotype": "gGETG",
"binary": "01010",
"value": 1.0556310301916847
},
{
"errors": null,
"id": 12,
"phenotype": 1.0152510120727598,
"genotype": "aAETG",
"binary": "10010",
"value": 1.0152510120727598
},
{
"errors": null,
"id": 13,
"phenotype": 1.0556310301916847,
"genotype": "gGKMG",
"binary": "01100",
"value": 1.0556310301916847
},
{
"errors": null,
"id": 14,
"phenotype": 1.0334809063896502,
"genotype": "aAKMG",
"binary": "10100",
"value": 1.0334809063896502
},
{
"errors": null,
"id": 15,
"phenotype": 1.0152510120727598,
"genotype": "aGEMG",
"binary": "11000",
"value": 1.0152510120727598
},
{
"errors": null,
"id": 16,
"phenotype": 1.113243817588169,
"genotype": "gAKTS",
"binary": "00111",
"value": 1.113243817588169
},
{
"errors": null,
"id": 17,
"phenotype": 1.113243817588169,
"genotype": "gGETS",
"binary": "01011",
"value": 1.113243817588169
},
{
"errors": null,
"id": 18,
"phenotype": 1.113243817588169,
"genotype": "aAETS",
"binary": "10011",
"value": 1.113243817588169
},
{
"errors": null,
"id": 19,
"phenotype": 1.1797097438793012,
"genotype": "gGKMS",
"binary": "01101",
"value": 1.1797097438793012
},
{
"errors": null,
"id": 20,
"phenotype": 1.113243817588169,
"genotype": "aAKMS",
"binary": "10101",
"value": 1.113243817588169
},
{
"errors": null,
"id": 21,
"phenotype": 1.113243817588169,
"genotype": "aGEMS",
"binary": "11001",
"value": 1.113243817588169
},
{
"errors": null,
"id": 22,
"phenotype": 1.044009502834679,
"genotype": "gGKTG",
"binary": "01110",
"value": 1.044009502834679
},
{
"errors": null,
"id": 23,
"phenotype": 1.0334809063896502,
"genotype": "aAKTG",
"binary": "10110",
"value": 1.0334809063896502
},
{
"errors": null,
"id": 24,
"phenotype": 1.0152510120727598,
"genotype": "aGETG",
"binary": "11010",
"value": 1.0152510120727598
},
{
"errors": null,
"id": 25,
"phenotype": 1.0931151178699843,
"genotype": "aGKMG",
"binary": "11100",
"value": 1.0931151178699843
},
{
"errors": null,
"id": 26,
"phenotype": 1.2233083203139679,
"genotype": "gGKTS",
"binary": "01111",
"value": 1.2233083203139679
},
{
"errors": null,
"id": 27,
"phenotype": 1.1797097438793012,
"genotype": "aAKTS",
"binary": "10111",
"value": 1.1797097438793012
},
{
"errors": null,
"id": 28,
"phenotype": 1.113243817588169,
"genotype": "aGETS",
"binary": "11011",
"value": 1.113243817588169
},
{
"errors": null,
"id": 29,
"phenotype": 1.1386104400539243,
"genotype": "aGKMS",
"binary": "11101",
"value": 1.1386104400539243
},
{
"errors": null,
"id": 30,
"phenotype": 1.0556310301916847,
"genotype": "aGKTG",
"binary": "11110",
"value": 1.0556310301916847
},
{
"errors": null,
"id": 31,
"phenotype": 1.3197838706452887,
"genotype": "aGKTS",
"binary": "11111",
"value": 1.3197838706452887
}
],
"links": [
{
"target": 1,
"mutation": "G4S",
"source": 0
},
{
"target": 2,
"mutation": "M3T",
"source": 0
},
{
"target": 3,
"mutation": "E2K",
"source": 0
},
{
"target": 4,
"mutation": "A1G",
"source": 0
},
{
"target": 5,
"mutation": "g0a",
"source": 0
},
{
"target": 8,
"mutation": "A1G",
"source": 1
},
{
"target": 9,
"mutation": "g0a",
"source": 1
},
{
"target": 0,
"mutation": "S4G",
"source": 1
},
{
"target": 6,
"mutation": "M3T",
"source": 1
},
{
"target": 7,
"mutation": "E2K",
"source": 1
},
{
"target": 0,
"mutation": "T3M",
"source": 2
},
{
"target": 10,
"mutation": "E2K",
"source": 2
},
{
"target": 11,
"mutation": "A1G",
"source": 2
},
{
"target": 12,
"mutation": "g0a",
"source": 2
},
{
"target": 6,
"mutation": "G4S",
"source": 2
},
{
"target": 0,
"mutation": "K2E",
"source": 3
},
{
"target": 10,
"mutation": "M3T",
"source": 3
},
{
"target": 13,
"mutation": "A1G",
"source": 3
},
{
"target": 14,
"mutation": "g0a",
"source": 3
},
{
"target": 7,
"mutation": "G4S",
"source": 3
},
{
"target": 0,
"mutation": "G1A",
"source": 4
},
{
"target": 8,
"mutation": "G4S",
"source": 4
},
{
"target": 11,
"mutation": "M3T",
"source": 4
},
{
"target": 13,
"mutation": "E2K",
"source": 4
},
{
"target": 15,
"mutation": "g0a",
"source": 4
},
{
"target": 0,
"mutation": "a0g",
"source": 5
},
{
"target": 9,
"mutation": "G4S",
"source": 5
},
{
"target": 12,
"mutation": "M3T",
"source": 5
},
{
"target": 14,
"mutation": "E2K",
"source": 5
},
{
"target": 15,
"mutation": "A1G",
"source": 5
},
{
"target": 16,
"mutation": "E2K",
"source": 6
},
{
"target": 17,
"mutation": "A1G",
"source": 6
},
{
"target": 18,
"mutation": "g0a",
"source": 6
},
{
"target": 2,
"mutation": "S4G",
"source": 6
},
{
"target": 1,
"mutation": "T3M",
"source": 6
},
{
"target": 16,
"mutation": "M3T",
"source": 7
},
{
"target": 1,
"mutation": "K2E",
"source": 7
},
{
"target": 19,
"mutation": "A1G",
"source": 7
},
{
"target": 20,
"mutation": "g0a",
"source": 7
},
{
"target": 3,
"mutation": "S4G",
"source": 7
},
{
"target": 1,
"mutation": "G1A",
"source": 8
},
{
"target": 19,
"mutation": "E2K",
"source": 8
},
{
"target": 4,
"mutation": "S4G",
"source": 8
},
{
"target": 21,
"mutation": "g0a",
"source": 8
},
{
"target": 17,
"mutation": "M3T",
"source": 8
},
{
"target": 1,
"mutation": "a0g",
"source": 9
},
{
"target": 18,
"mutation": "M3T",
"source": 9
},
{
"target": 20,
"mutation": "E2K",
"source": 9
},
{
"target": 21,
"mutation": "A1G",
"source": 9
},
{
"target": 5,
"mutation": "S4G",
"source": 9
},
{
"target": 16,
"mutation": "G4S",
"source": 10
},
{
"target": 2,
"mutation": "K2E",
"source": 10
},
{
"target": 3,
"mutation": "T3M",
"source": 10
},
{
"target": 22,
"mutation": "A1G",
"source": 10
},
{
"target": 23,
"mutation": "g0a",
"source": 10
},
{
"target": 24,
"mutation": "g0a",
"source": 11
},
{
"target": 17,
"mutation": "G4S",
"source": 11
},
{
"target": 2,
"mutation": "G1A",
"source": 11
},
{
"target": 4,
"mutation": "T3M",
"source": 11
},
{
"target": 22,
"mutation": "E2K",
"source": 11
},
{
"target": 24,
"mutation": "A1G",
"source": 12
},
{
"target": 2,
"mutation": "a0g",
"source": 12
},
{
"target": 18,
"mutation": "G4S",
"source": 12
},
{
"target": 5,
"mutation": "T3M",
"source": 12
},
{
"target": 23,
"mutation": "E2K",
"source": 12
},
{
"target": 19,
"mutation": "G4S",
"source": 13
},
{
"target": 25,
"mutation": "g0a",
"source": 13
},
{
"target": 3,
"mutation": "G1A",
"source": 13
},
{
"target": 4,
"mutation": "K2E",
"source": 13
},
{
"target": 22,
"mutation": "M3T",
"source": 13
},
{
"target": 25,
"mutation": "A1G",
"source": 14
},
{
"target": 3,
"mutation": "a0g",
"source": 14
},
{
"target": 20,
"mutation": "G4S",
"source": 14
},
{
"target": 5,
"mutation": "K2E",
"source": 14
},
{
"target": 23,
"mutation": "M3T",
"source": 14
},
{
"target": 24,
"mutation": "M3T",
"source": 15
},
{
"target": 25,
"mutation": "E2K",
"source": 15
},
{
"target": 4,
"mutation": "a0g",
"source": 15
},
{
"target": 5,
"mutation": "G1A",
"source": 15
},
{
"target": 21,
"mutation": "G4S",
"source": 15
},
{
"target": 26,
"mutation": "A1G",
"source": 16
},
{
"target": 27,
"mutation": "g0a",
"source": 16
},
{
"target": 10,
"mutation": "S4G",
"source": 16
},
{
"target": 6,
"mutation": "K2E",
"source": 16
},
{
"target": 7,
"mutation": "T3M",
"source": 16
},
{
"target": 8,
"mutation": "T3M",
"source": 17
},
{
"target": 26,
"mutation": "E2K",
"source": 17
},
{
"target": 11,
"mutation": "S4G",
"source": 17
},
{
"target": 28,
"mutation": "g0a",
"source": 17
},
{
"target": 6,
"mutation": "G1A",
"source": 17
},
{
"target": 9,
"mutation": "T3M",
"source": 18
},
{
"target": 27,
"mutation": "E2K",
"source": 18
},
{
"target": 28,
"mutation": "A1G",
"source": 18
},
{
"target": 6,
"mutation": "a0g",
"source": 18
},
{
"target": 12,
"mutation": "S4G",
"source": 18
},
{
"target": 8,
"mutation": "K2E",
"source": 19
},
{
"target": 26,
"mutation": "M3T",
"source": 19
},
{
"target": 13,
"mutation": "S4G",
"source": 19
},
{
"target": 29,
"mutation": "g0a",
"source": 19
},
{
"target": 7,
"mutation": "G1A",
"source": 19
},
{
"target": 9,
"mutation": "K2E",
"source": 20
},
{
"target": 27,
"mutation": "M3T",
"source": 20
},
{
"target": 29,
"mutation": "A1G",
"source": 20
},
{
"target": 14,
"mutation": "S4G",
"source": 20
},
{
"target": 7,
"mutation": "a0g",
"source": 20
},
{
"target": 8,
"mutation": "a0g",
"source": 21
},
{
"target": 9,
"mutation": "G1A",
"source": 21
},
{
"target": 28,
"mutation": "M3T",
"source": 21
},
{
"target": 29,
"mutation": "E2K",
"source": 21
},
{
"target": 15,
"mutation": "S4G",
"source": 21
},
{
"target": 26,
"mutation": "G4S",
"source": 22
},
{
"target": 10,
"mutation": "G1A",
"source": 22
},
{
"target": 11,
"mutation": "K2E",
"source": 22
},
{
"target": 13,
"mutation": "T3M",
"source": 22
},
{
"target": 30,
"mutation": "g0a",
"source": 22
},
{
"target": 10,
"mutation": "a0g",
"source": 23
},
{
"target": 27,
"mutation": "G4S",
"source": 23
},
{
"target": 12,
"mutation": "K2E",
"source": 23
},
{
"target": 14,
"mutation": "T3M",
"source": 23
},
{
"target": 30,
"mutation": "A1G",
"source": 23
},
{
"target": 28,
"mutation": "G4S",
"source": 24
},
{
"target": 11,
"mutation": "a0g",
"source": 24
},
{
"target": 12,
"mutation": "G1A",
"source": 24
},
{
"target": 30,
"mutation": "E2K",
"source": 24
},
{
"target": 15,
"mutation": "T3M",
"source": 24
},
{
"target": 30,
"mutation": "M3T",
"source": 25
},
{
"target": 29,
"mutation": "G4S",
"source": 25
},
{
"target": 13,
"mutation": "a0g",
"source": 25
},
{
"target": 14,
"mutation": "G1A",
"source": 25
},
{
"target": 15,
"mutation": "K2E",
"source": 25
},
{
"target": 16,
"mutation": "G1A",
"source": 26
},
{
"target": 17,
"mutation": "K2E",
"source": 26
},
{
"target": 19,
"mutation": "T3M",
"source": 26
},
{
"target": 22,
"mutation": "S4G",
"source": 26
},
{
"target": 31,
"mutation": "g0a",
"source": 26
},
{
"target": 16,
"mutation": "a0g",
"source": 27
},
{
"target": 18,
"mutation": "K2E",
"source": 27
},
{
"target": 23,
"mutation": "S4G",
"source": 27
},
{
"target": 20,
"mutation": "T3M",
"source": 27
},
{
"target": 31,
"mutation": "A1G",
"source": 27
},
{
"target": 24,
"mutation": "S4G",
"source": 28
},
{
"target": 17,
"mutation": "a0g",
"source": 28
},
{
"target": 18,
"mutation": "G1A",
"source": 28
},
{
"target": 21,
"mutation": "T3M",
"source": 28
},
{
"target": 31,
"mutation": "E2K",
"source": 28
},
{
"target": 25,
"mutation": "S4G",
"source": 29
},
{
"target": 19,
"mutation": "a0g",
"source": 29
},
{
"target": 20,
"mutation": "G1A",
"source": 29
},
{
"target": 21,
"mutation": "K2E",
"source": 29
},
{
"target": 31,
"mutation": "M3T",
"source": 29
},
{
"target": 24,
"mutation": "K2E",
"source": 30
},
{
"target": 25,
"mutation": "T3M",
"source": 30
},
{
"target": 31,
"mutation": "G4S",
"source": 30
},
{
"target": 22,
"mutation": "a0g",
"source": 30
},
{
"target": 23,
"mutation": "G1A",
"source": 30
},
{
"target": 26,
"mutation": "a0g",
"source": 31
},
{
"target": 27,
"mutation": "G1A",
"source": 31
},
{
"target": 28,
"mutation": "K2E",
"source": 31
},
{
"target": 29,
"mutation": "T3M",
"source": 31
},
{
"target": 30,
"mutation": "S4G",
"source": 31
}
],
"multigraph": false,
"graph": []
}
{
"target": 31,
"source": 0,
"paths": [
{
"index": 1,
"weight": 7.597396320212795,
"rank": 1,
"nodes": [
0,
1,
7,
19,
26,
31
]
},
{
"index": 2,
"weight": 5.58724865840025,
"rank": 2,
"nodes": [
0,
1,
6,
16,
26,
31
]
},
{
"index": 3,
"weight": 2.1972245773362196,
"rank": 3,
"nodes": [
0,
3,
10,
22,
26,
31
]
},
{
"index": 4,
"weight": 6.150602768446279,
"rank": 4,
"nodes": [
0,
1,
8,
19,
26,
31
]
},
{
"index": 5,
"weight": 3.4657359027997265,
"rank": 5,
"nodes": [
0,
3,
10,
16,
26,
31
]
},
{
"index": 6,
"weight": 5.8971538676367405,
"rank": 6,
"nodes": [
0,
1,
6,
18,
27,
31
]
},
{
"index": 7,
"weight": 2.9444389791664403,
"rank": 7,
"nodes": [
0,
3,
14,
25,
29,
31
]
},
{
"index": 8,
"weight": 6.0473721790462776,
"rank": 8,
"nodes": [
0,
1,
6,
17,
26,
31
]
},
{
"index": 9,
"weight": 4.969813299576001,
"rank": 9,
"nodes": [
0,
1,
8,
21,
29,
31
]
},
{
"index": 10,
"weight": 6.429719478039138,
"rank": 10,
"nodes": [
0,
3,
7,
19,
26,
31
]
},
{
"index": 11,
"weight": 3.5553480614894135,
"rank": 11,
"nodes": [
0,
3,
13,
25,
29,
31
]
},
{
"index": 12,
"weight": 5.093750200806762,
"rank": 12,
"nodes": [
0,
1,
6,
16,
27,
31
]
},
{
"index": 13,
"weight": 0,
"rank": 13,
"nodes": [
0,
3,
10,
22,
30,
31
]
},
{
"index": 14,
"weight": 5.198497031265826,
"rank": 14,
"nodes": [
0,
3,
13,
19,
26,
31
]
},
{
"index": 15,
"weight": 3.4339872044851463,
"rank": 15,
"nodes": [
0,
3,
14,
20,
27,
31
]
},
{
"index": 16,
"weight": 5.10594547390058,
"rank": 16,
"nodes": [
0,
1,
8,
17,
26,
31
]
},
{
"index": 17,
"weight": 2.3978952727983707,
"rank": 17,
"nodes": [
0,
3,
14,
20,
29,
31
]
},
{
"index": 18,
"weight": 3.091042453358316,
"rank": 18,
"nodes": [
0,
3,
10,
16,
27,
31
]
}
]
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment