dna.yml

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# Common DNA models in YAML format     #
# Copyright (c) 2018 by Bui Quang Minh #
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substitutionModels:

### JC model ###
- name: JC
  description: Jukes-Cantor model
  citation: “Jukes and Cantor, 1969”
  reversible: true
  stateFrequency: [ 0.25, 0.25, 0.25, 0.25 ]
  rateMatrix:
  - [ -, 1, 1, 1 ]
  - [ 1, -, 1, 1 ]
  - [ 1, 1, -, 1 ]
  - [ 1, 1, 1, - ]

### GTR model ###
- name: GTR
  description: “General time reversible”
  citation: “Tavare, 1986”
  reversible: true
  parameters:
  - name: r[1..5]  # rate parameter vector r[1], ..., r[5]
    range: [ 0.0001, 100 ]
    initValue: 1.0
  - name: f[1..4]  # frequency vector f[1],..., f[4]
    type: frequency  # make parameters in range [0,1] and sum to 1.0

  rateMatrix:
  - [         -, r[1]*f[2], r[2]*f[3], r[3]*f[4] ]
  - [ r[1]*f[1],         -, r[4]*f[3], r[5]*f[4] ]
  - [ r[2]*f[1], r[4]*f[2],         -,      f[4] ]
  - [ r[3]*f[1], r[5]*f[2],      f[3],         - ]

  stateFrequency: [ f ]