bistro-bio 0.6.0 (latest) · OCaml Package

type matrix = [

| `DAYHOFF
| `DCMUT
| `JTT
| `MTREV
| `WAG
| `RTREV
| `CPREV
| `VT
| `BLOSUM62
| `MTMAM
| `LG
| `MTART
| `MTZOA
| `PMB
| `HIVB
| `HIVW
| `JTTDCMUT
| `FLU
| `STMTREV
| `DUMMY
| `DUMMY2
| `AUTO
| `LG4M
| `LG4X
| `PROT_FILE
| `GTR_UNLINKED
| `GTR

]

type bin_model = [

| `BINCAT
| `BINCATI
| `ASC_BINCAT
| `BINGAMMA
| `ASC_BINGAMMA
| `BINGAMMAI

]

type nucleotide_model = [

| `GTRCAT
| `GTRCATI
| `ASC_GTRCAT
| `GTRGAMMA
| `ASC_GTRGAMMA
| `GTRGAMMAI

]

type multi_state_model = [

| `MULTICAT
| `MULTICATI
| `ASC_MULTICAT
| `MULTIGAMMA
| `ASC_MULTIGAMMA
| `MULTIGAMMAI

]

type amino_acid_model = [

| `PROTCAT of matrix
| `ASC_PROTCAT of matrix
| `PROTGAMMA of matrix

]

type model = [

| bin_model
| nucleotide_model
| multi_state_model
| amino_acid_model
| `X of [ bin_model | nucleotide_model | multi_state_model | amino_acid_model ]
| `F of amino_acid_model

]

val hpc_fasta : 
  ?b:int ->
  ?c:int ->
  ?d:bool ->
  ?_D_:bool ->
  ?f:
    [< `A
    | `B
    | `C
    | `D
    | `E
    | `F
    | `G
    | `H
    | `I
    | `J
    | `N
    | `R
    | `S
    | `T
    | `V
    | `W
    | `a
    | `b
    | `c
    | `d
    | `e
    | `g
    | `h
    | `i
    | `j
    | `k
    | `m
    | `n
    | `o
    | `p
    | `q
    | `r
    | `s
    | `t
    | `u
    | `v
    | `w
    | `x
    | `y ] ->
  ?_F_:bool ->
  ?k:bool ->
  ?p:int ->
  ?t:Formats.newick Bistro.file ->
  ?_T_:int ->
  ?no_bgfs:bool ->
  model ->
  Formats.fasta Bistro.file ->
  [ `raxmlHPC ] Bistro.directory

val hpc_phylip : 
  ?b:int ->
  ?c:int ->
  ?d:bool ->
  ?_D_:bool ->
  ?f:
    [< `A
    | `B
    | `C
    | `D
    | `E
    | `F
    | `G
    | `H
    | `I
    | `J
    | `N
    | `R
    | `S
    | `T
    | `V
    | `W
    | `a
    | `b
    | `c
    | `d
    | `e
    | `g
    | `h
    | `i
    | `j
    | `k
    | `m
    | `n
    | `o
    | `p
    | `q
    | `r
    | `s
    | `t
    | `u
    | `v
    | `w
    | `x
    | `y ] ->
  ?_F_:bool ->
  ?k:bool ->
  ?p:int ->
  ?t:Formats.newick Bistro.file ->
  ?_T_:int ->
  ?no_bgfs:bool ->
  model ->
  Formats.phylip Bistro.file ->
  [ `raxmlHPC ] Bistro.directory

val result : [ `raxmlHPC ] Bistro.directory -> Formats.newick Bistro.file

val best_tree : [ `raxmlHPC ] Bistro.directory -> Formats.newick Bistro.file

val distances : [ `raxmlHPC ] Bistro.directory -> Bistro.text Bistro.file

package bistro-bio