orthomam.mli 1.99 KB
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open Codepitk
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open Bistro
open File_formats

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type alignment
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val alignments_of_db :
  Orthomam_db.t ->
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  alignment list

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type query
val query :
  alignment ->
  convergent_species:string list workflow ->
  query

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val family_id : query -> string

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val alignment : query -> phylip file
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val nucleotide_alignment : query -> nucleotide_fasta file

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val tree_of_db :
  Orthomam_db.t ->
  branch_length_unit:[`Nucleotide | `Amino_acid | `Codon] ->
  convergent_species:string list ->
  nhx file

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val tree :
  branch_length_unit:[`Nucleotide | `Amino_acid | `Codon] ->
  query ->
  nhx file
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include Detection_pipeline.S with type query := query
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val species_with_echolocation : string list
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val prestin : Orthomam_db.t -> query

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val ensembl_tree : newick file
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val compare_tree_branch_lengths :
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  nhx file ->
  nhx file ->
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  pdf file
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val number_of_missing_sequences_repartition :
  Orthomam_db.t ->
  pdf file

val concatenate :
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  ?nmissing:int ->
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  ?seed:int ->
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  Orthomam_db.t ->
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  int ->
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  phylip file
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(** Produces a concatenate of gene alignments in a
   database. Alignments where strictly more than
   [max_missing_sequences] leaves are missing are discarded, as well
   as those which show defects following [Orthomam_db.check_orf]
   (except for stop codons at last position, which are tolerated. When
   using [site_sampling], (nucleotidic) sites are randomly selected
   and concatenated. Note that in that case the codon structure is
   lost. *)
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val concatenate_calibration :
  seed:int ->
  Orthomam_db.t ->
  pdf file
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val estimated_nucleotide_tree :
  Orthomam_db.t ->
  newick file
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val estimated_codon_tree :
  Orthomam_db.t ->
  newick file

val estimated_amino_acid_tree :
  Orthomam_db.t ->
  newick file
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val convergence_species_tree_pdf :
  convergent_species:string list ->
  Orthomam_db.t ->
  pdf file
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val site_ranking :
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  ?subset:int ->
  meth:[`multinomial_asymptotic_lrt | `tdg09] ->
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  convergent_species:string list ->
  Orthomam_db.t ->
  Candidate_site.t list workflow
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val draw_site : query -> int -> pdf file