detection_pipeline.mli 1.51 KB
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open Bistro
open File_formats

module type Query = sig
  type t
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  val tree :
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    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

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  include Query with type t := query

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

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  val identical : query -> cpt file
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  val topological : query -> cpt file
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  val multinomial_simulation_lrt : query -> cpt file
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  val multinomial_simulation_sparse : query -> cpt file
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  val multinomial_asymptotic_lrt : query -> cpt file
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  val multinomial_asymptotic_sparse : query -> cpt file
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  val tdg09 : query -> cpt file
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  val failsafe_tdg09 : query -> cpt file
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  val inhouse_tdg09 : query -> cpt file

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  val pcoc : ?gamma:bool -> ?ncat:int -> query -> cpt file
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  val pcoc_v2 :
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    ?gamma:bool -> ?aa_profiles:Pcoc.aa_profiles -> query -> cpt file
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  val gemma :
    query ->
    lmm_test:[ `All | `LRT | `Score | `Wald ] ->
    relatedness_mode:[ `Centered | `Standardized ] ->
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    cpt file
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  val inhouse_lmm : query -> cpt file
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  val diffsel : query -> cpt file
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  val diffseldsparse :
    ?pi:float ->
    ?shiftprob:float * float ->
    ?eps:float ->
    query ->
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    cpt file
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  val view_site :
    query -> convergent_species:string list -> site_pos:int -> pdf file
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end

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