detection_pipeline.mli 1.3 KB
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open Bistro
open File_formats

module type Query = sig
  type t
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  val tree :
    branch_length_unit:[`Nucleotide | `Amino_acid | `Codon] ->
    t -> nhx file
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  val nucleotide_alignment : t -> nucleotide_fasta file
end

module type S = sig
  type query

  val amino_acid_alignment : query -> aminoacid_fasta file
  val gene_tree : query -> nw file
  val dn_tree : query -> text file
  val ds_tree : query -> text file
  val dnds_tree : query -> text file

  val identical : query -> text file
  val topological : query -> text file
  val multinomial : query -> text file
  val multinomial_simulation_lrt : query -> text file
  val multinomial_simulation_sparse : query -> text file
  val multinomial_asymptotic_lrt : query -> text file
  val multinomial_asymptotic_sparse : query -> text file
  val tdg09 : query -> text file
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  val failsafe_tdg09 : query -> text file
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  val pcoc : ?gamma:bool -> ?ncat:int -> query -> text file
  val pcoc_v2 :
    ?gamma:bool ->
    ?aa_profiles:Pcoc.aa_profiles ->
    query -> text file
  val diffsel : query -> text file
  val diffseldsparse :
    ?pi:float ->
    ?shiftprob:float * float ->
    ?eps:float ->
    query ->
    text file
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  val view_site : 
    query -> 
    convergent_species:string list -> 
    site_pos:int -> 
    pdf file
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end

module Make(Q : Query) : S with type query := Q.t