bielawski.yml

---
### Following models are prepared by Joe Bielawski ###

substitutionModels:

- name: BG02
  description: strand symmetric DNA substitution model
  citation: “Bielawski and Gold, 2002”
  reversible: false
  numStates: 4
  order: [T, C, A, G]

  parameters:
  - name: [ c1, c2, x1, x2, x3, x4 ]
    # c1: T->C = A->G (on A-strand)
    # c2: C->T = G->A (on A-strand)
    # x1: T->A = A->T
    # x2: T->G = G->T
    # x3: C->A = A->C
    # x4: C->G = G->C
    type: substitutionRate

  rateMatrix:
    - [ -, c1, x1, x2 ]
    - [ c2, -, x3, x4 ]
    - [ x1, x2, -, c1 ]
    - [ x3, x4, c2, - ]


- name: M0.free
  reversible: true
  numStates: 61
  # BQM: Don't use geneticCode, instead use forData
  #geneticCode: NCBI
  forData: Codon2
  parameters:
  - name: w
    description: dN/dS rate ratio
    range:[ 0.0001, 1.0 ]
  - name: k
    description: Ts/Tv rate ratio
  - name: f[1..61]
    description: Codon state frequency
    type: frequency  #this needs to be more specific!
  rateMatrix:  
  # JB: This will need to be big; maybe read from another file?
  # BQM: better specifying everything here!
    - [   -, k*f[2], w*f[3], k*w*f[4],  … (61)]
    - [ k*f[1],   -, w*f[3],  w*f[4],  … (61)]
    - [ w*f[1], w*f[2],   -,  0.0,  … (61)]
    - [ w*f[1], w*f[2], k*f[3],    -,  … (61)]
    -  …
    - [(61),   0,   0,    0,  … (61)]


- name: M0.wfixed
  fromModel: M0.free
  constraints:
  - w = 1.0

### RaMoSS model of Jones et al., 2018 ### 

- name: CLM3a
  description: Covarion-like Model 3
  citation: “Jones et al., 2016”
  reversible: true
  #geneticCode: NCBI2
  forData: Codon2
  parameters:
  # BQM: no need to do this
  #- using: [M0.free, M0.fixed]
  - name: d
    description: covarion switching rate
    range:[ 0.0001, 10.0 ]
  - name: [ pM0, pM0fixed ]
    type: frequency  # make sum=1.0
  covarion:  
  - fromModel: M0.free
  - name: XXX
  - name: YYY
  - fromModel: M0.fixed


### RaMoSS model of Jones et al., 2018 ### 
- name: RaMoSS
  description: Covarion-like Model 3
  citation: “Jones et al., 2018”
  reversible: true
  forData: Codon2
  mixture:
  - fromModel: M0.free
    weight: w1
  - fromModel: M0.fixed
    weight: w2
  - fromModel: CLM3a
    weight: w3
 
  # BQM: This mixture model has 3 components with different Q matrix sizes??