package bistro-bio

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package bistro-bio
Legend:
Library
Module
Module type
Parameter
Class
Class type
type sequence_type = [
  1. | `DNA
  2. | `AA
  3. | `BIN
  4. | `MORPH
  5. | `CODON of int
  6. | `NT2AA
]
type dna_model = [
  1. | `JC69
  2. | `F81
  3. | `K80
  4. | `HKY85
  5. | `TN93
  6. | `TNe
  7. | `K81
  8. | `K81u
  9. | `TPM2
  10. | `TPM2u
  11. | `TPM3
  12. | `TPM3u
  13. | `TIM
  14. | `TIMe
  15. | `TIM2
  16. | `TIM2e
  17. | `TIM3
  18. | `TIM3e
  19. | `TVM
  20. | `TVMe
  21. | `SYM
  22. | `GTR
]
type protein_model = [
  1. | `BLOSUM62
  2. | `cpREV
  3. | `Dayhoff
  4. | `DCMut
  5. | `FLU
  6. | `HIVb
  7. | `HIVw
  8. | `JTT
  9. | `JTTDCMut
  10. | `LG
  11. | `mtART
  12. | `mtMAM
  13. | `mtREV
  14. | `mtZOA
  15. | `mtMet
  16. | `mtVer
  17. | `mtInv
  18. | `Poisson
  19. | `PMB
  20. | `rtREV
  21. | `VT
  22. | `WAG
]
type protein_mixture_model = [
  1. | `C10
  2. | `C20
  3. | `C30
  4. | `C40
  5. | `C50
  6. | `C60
  7. | `EX2
  8. | `EX3
  9. | `EHO
  10. | `UL2
  11. | `UL3
  12. | `EX_EHO
  13. | `LG4M
  14. | `LG4X
  15. | `CF4
]
type codon_model = [
  1. | `MG
  2. | `MGK
  3. | `MG1KTS
  4. | `MG1KTV
  5. | `MG2K
  6. | `GY
  7. | `GY1KTS
  8. | `GY1KTV
  9. | `GY2K
  10. | `ECMK07
  11. | `ECMrest
  12. | `ECMS05
]
type binary_model = [
  1. | `JC2
  2. | `GTR2
]
type freq_type = [
  1. | `F
  2. | `FO
  3. | `FQ
  4. | `F1x4
  5. | `F3x4
]
type rate_type = [
  1. | `I
  2. | `G of int option
  3. | `I_G
  4. | `R of int option
  5. | `I_R
]
type model_spec
val model_spec : ?freq_type:freq_type -> ?rate_type:rate_type -> [ dna_model | protein_model | protein_mixture_model | codon_model | binary_model ] -> model_spec
val iqtree : ?t:[ `BIONJ | `RANDOM | `Tree of Formats.newick Bistro.file ] -> ?te:Formats.newick Bistro.file -> ?o:string -> ?nt:int -> ?seed:int -> ?n:int -> ?m:model_spec -> ?z:Formats.newick Bistro.file -> ?st:sequence_type -> ?spp:Formats.nexus Bistro.file -> ?keep_ident:bool -> [ `phylip of Formats.phylip Bistro.file | `fasta of Formats.fasta Bistro.file ] -> [ `iqtree ] Bistro.directory
val treefile : [ `iqtree ] Bistro.directory -> Formats.newick Bistro.file
val report : [ `iqtree ] Bistro.directory -> Bistro.text Bistro.file