CancerEvolModel_tri.yml

# Substitution cancer model definition
# https://github.com/bqminh/phylomodel


dataTypes:
#### definition for DNA data ###
- name: TriNucleotide
  states: [ A, C, G, T, R, Y, S, W, K, M, B, D, H, V, N ]
  missing: [ ? ]
  gap: [ - ]

substitutionModels:

### CEM model ###
# r[1] u_AG
# r[2] u_AT
# r[3] u_AC
# r[4] u_CT
# r[5] u_CG
# r[6] u_CA
# r[7] u_GA
# r[8] u_GC
# r[9] u_GT
# r[10] u_TC
# r[11] u_TA
# r[12] u_TG
- name: CEM3
  description: “a Cancer Evolutionary Model”
  reversible: false
  parameters:
  - name: r[1..12]  # rate parameter vector
    range: [ 0.0001, 100 ]
    initValue: 1.0
  - name: d  # deletion/loss rate parameter
    range: [ 0.0001, 100 ]
    initValue: 1.0

  rateMatrix:
  - [ -,	0,	 0,	  0,	  r[1],		 0,		0,		r[2],		0,		r[3],		0,		0,	    0,		0,		0	]
  - [ 0,	-,	 0,	  0,	  0,		 r[4],		r[5],		0,		0,		r[6],		0,		0,	    0,		0,		0	]
  - [ 0,	0,	 -,	  0,	  r[7],		 0,		r[8],		0,		r[9],		0,		0,		0,	    0,		0,		0	]
  - [ 0,	0,	 0,	  -,	  0,		 r[10],		0,		r[11],		r[12],		0,		0,		0,	    0,		0,		0	]
  - [ r[7]+d,	0,	 r[1]+d,  0,	  -,		 0,		r[3],		r[9],		r[2],		r[8],		0,		r[2]+r[9],  0,		r[3]+r[8],	0	]
  - [ 0,	r[10]+d, 0,	  r[4]+d, 0,		 -,		r[12],		r[6],		r[5],		r[11],		r[5]+r[12],	0,	    r[6]+r[11], 0,		0	]
  - [ 0,	r[8]+d,	 r[5]+d,  0,	  r[6],		 r[9],		-,		0,		r[4],		r[7],		r[9]+r[4],  	0,	    0,		r[7]+r[6],	0	]
  - [ r[11]+d,  0,	 0,	  r[2]+d, r[12],	 r[3],		0,		-,		r[1],		r[10],		0,		r[1]+r[12], r[3]+r[10], 0,		0	]
  - [ 0,	0,	 r[12]+d, r[9]+d, r[11],	 r[8],		r[10],		r[7],		-,		0,		r[8]+r[10],	r[7]+r[11], 0,		0,		0	]
  - [ r[6]+d,	r[3]+d,	 0,	  0,	  r[5],		 r[2],		r[1],		r[4],		0,		-,		0,		0,	    r[2]+r[4],  r[1]+r[5],	0	]
  - [ 0,	0,	 0,	  0,	  0,		 d+r[8]+r[9],	d+r[10]+r[12],	0,		d+r[4]+r[5],	0,		-,		r[6],	    r[7],	r[11],		0	]
  - [ 0,	0,	 0,	  0,	  d+r[11]+r[12], 0,		0,		d+r[7]+r[9],	d+r[1]+r[2],	0,		r[3],		-,	    r[8],	r[10],		0	]
  - [ 0,	0,	 0,	  0,	  0,		 d+r[3]+r[2],	0,		d+r[6]+r[4],	0,		d+r[10]+r[11],	r[1],		r[5],	    -,		r[12],		0	]
  - [ 0,	0,	 0,	  0,	  d+r[5]+r[6],	 0,		d+r[1]+r[3],	0,		0,		d+r[7]+r[8],	r[2],		r[4],	    r[9],	-,		0	]
  - [ 0,	0,	 0,	  0,	  0,		 0,		0,		0,		0,		0,		d,		d,	    d,		d,		-	]