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Module: SequenceEvolution

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Niema Moshiri edited this page May 9, 2020 · 32 revisions

The SequenceEvolution module evolves the sequences of the viruses within a specified node until a specified time. See the source code to see what is defined by the abstract class.

List of Implementations

SequenceEvolution_EmpiricalCodonModelPyvolve

  • Uses Pyvolve to simulate sequence evolution on the generated phylogenetic trees under an Empirical Codon Model (ECM)
  • See Section 6.5 of the Pyvolve user manual for more information
  • Requirements:
  • Config Parameters:
    • ecm_type: Desired ECM type to use ("restricted" or "unrestricted")
    • ecm_alpha: Desired ECM alpha parameter (or "" for default)
    • ecm_beta: Desired ECM beta parameter (or "" for default)
    • ecm_omega: Desired ECM omega parameter (or "" for default)
    • ecm_codon_frequencies_dictionary: Desired codon frequencies (excluding STOP codons), or an empty dictionary (i.e., {}) to use default model parameters

SequenceEvolution_GTRCodonSeqGen

  • Uses Seq-Gen to simulate sequence evolution on the generated phylogenetic trees using a GTR Codon model
  • Requirements:
  • Config Parameters:
    • seqgen_path: The path to your seq-gen executable (or simply "seq-gen" if it is in your PATH variable)
    • seqgen_a_to_c: The desired transition rate from A to C (and C to A)
    • seqgen_a_to_g: The desired transition rate from A to G (and G to A)
    • seqgen_a_to_t: The desired transition rate from A to T (and T to A)
    • seqgen_c_to_g: The desired transition rate from C to G (and G to C)
    • seqgen_c_to_t: The desired transition rate from C to T (and T to C)
    • seqgen_g_to_t: The desired transition rate from G to T (and T to G)
    • seqgen_freq_a: The desired frequency of A
    • seqgen_freq_c: The desired frequency of C
    • seqgen_freq_g: The desired frequency of G
    • seqgen_freq_t: The desired frequency of T
    • seqgen_codon_site1_rate: The desired rate of heterogeneity for site 1 of a codon
    • seqgen_codon_site2_rate: The desired rate of heterogeneity for site 2 of a codon
    • seqgen_codon_site3_rate: The desired rate of heterogeneity for site 3 of a codon

SequenceEvolution_GTRGammaSeqGen

  • Uses Seq-Gen to simulate sequence evolution on the generated phylogenetic trees using the GTR+Γ model
  • Requirements:
  • Config Parameters:
    • seqgen_path: The path to your seq-gen executable (or simply "seq-gen" if it is in your PATH variable)
    • seqgen_a_to_c: The desired transition rate from A to C (and C to A)
    • seqgen_a_to_g: The desired transition rate from A to G (and G to A)
    • seqgen_a_to_t: The desired transition rate from A to T (and T to A)
    • seqgen_c_to_g: The desired transition rate from C to G (and G to C)
    • seqgen_c_to_t: The desired transition rate from C to T (and T to C)
    • seqgen_g_to_t: The desired transition rate from G to T (and T to G)
    • seqgen_freq_a: The desired frequency of A
    • seqgen_freq_c: The desired frequency of C
    • seqgen_freq_g: The desired frequency of G
    • seqgen_freq_t: The desired frequency of T
    • seqgen_gamma_shape: The desired shape parameter of the gamma model of rate heterogeneity
    • seqgen_num_gamma_rate_categories: The desired number of rate categories approximating the gamma model of rate heterogeneity (or simply "" to use the default of continuous)

SequenceEvolution_MechanisticCodonModelPyvolve

  • Uses Pyvolve to simulate sequence evolution on the generated phylogenetic trees under an Mechanistic Codon Model (MCM)
  • See Section 6.3 of the Pyvolve user manual for more information
  • Requirements:
  • Config Parameters:
    • mcm_type: Desired MCM type to use ("GY" or "MG")
    • mcm_alpha: Desired MCM alpha parameter (or "" for default)
    • mcm_beta: Desired MCM beta parameter (or "" for default)
    • mcm_omega: Desired MCM omega parameter (or "" for default)
      • Must specify a non-default value for either mcm_beta or mcm_omega (or both)
    • mcm_kappa: Desired transition-to-transversion ratio (or "" for default)
    • mcm_codon_frequencies_dictionary: Desired codon frequencies (excluding STOP codons), or an empty dictionary (i.e., {}) to use default model parameters
    • mcm_mutation_rates_dictionary: Desired mutation rates, or an empty dictionary (i.e., {}) to use default model
      • Cannot specify non-default for both mcm_kappa and mcm_mutation_rates_dictionaryparameters

SequenceEvolution_NoMutation

  • No mutations occur (i.e., each child perfectly inherits its parent's sequence)
  • Requirements:
    • None
  • Config Parameters:
    • None

SequenceEvolution_NoSeqs

SequenceEvolution_NucleotideModelPyvolve

  • Uses Pyvolve to simulate sequence evolution on the generated phylogenetic trees under a Nucleotide Model
  • See Section 6.1 of the Pyvolve user manual for more information
  • Requirements:
  • Config Parameters:
    • nuc_kappa: Desired transition-to-transversion ratio (or "" for default)
    • nuc_frequencies_dictionary: Desired nucleotide frequencies, or an empty dictionary (i.e., {}) to use default model parameters
    • nuc_mutation_rates_dictionary: Desired mutation rates, or an empty dictionary (i.e., {}) to use default model
      • Cannot specify non-default for both nuc_kappa and nuc_mutation_rates_dictionaryparameters

SequenceEvolution_PANGEA

SequenceEvolution_Pyvolve

  • Uses Pyvolve to simulate sequence evolution on the generated phylogenetic trees
    • We recommend using one of the other Pyvolve SequenceEvolution module implementations instead of this one. This one exists for advanced users to have full reign over Pyvolve model parameters
  • See the header comment in the source code as well as the Pyvolve user manual for usage information
  • Requirements:
  • Config Parameters:
    • pyvolve_model_type: Desired Pyvolve model type to use (see Pyvolve manual for valid options)
    • pyvolve_custom_model_parameters_dictionary: Custom-parameters dictionary for the selected model, as described in the Pyvolve manual, or an empty dictionary (i.e., {}) to use default model parameters
    • pyvolve_state_frequencies_class: Desired Pyvolve StateFrequencies class to use (see Pyvolve manual for valid options)
    • pyvolve_state_frequencies_parameters_dictionary: Dictionary storing selected StateFrequency class's desired parameters, in which the key of a key-value pair is a string representing the parameter's name, and the value is the parameter value (see Pyvolve manual for information)

SequenceEvolution_SeqGen

  • Uses Seq-Gen to simulate sequence evolution on the generated phylogenetic trees
  • Requirements:
  • Config Parameters:
    • seqgen_path: The path to your seq-gen executable (or simply "seq-gen" if it is in your PATH variable)
    • seqgen_args: The command line arguments to seq-gen
      • Do not specify -d, -k, -l, -n, -o, -p, or -s

Niema Moshiri & Siavash Mirarab 2016

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