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Commit 4a7cbafd authored by Louis Duchemin's avatar Louis Duchemin

Orthomam : add type annotations to clip_tree_on_alignment

parent cf04dbb7
......@@ -55,7 +55,7 @@ let remove_unobserved_sequences_from_alignment phylip : phylip file =
in
Workflow.path_plugin ~descr:"orthomam.remove_unobserved_sequences_from_alignment" f
let clip_tree_on_alignment tree ali =
let clip_tree_on_alignment (tree:(#newick as 'a) file) (ali: phylip file) : 'a file =
let f = fun%workflow dest ->
let open Phylogenetics in
let tree = Newick.from_file [%path tree] in
......@@ -613,9 +613,6 @@ let rer_converge ?max_read ?transform ?weighted ?scale ?continuous ~db
List.map
~f:(fun q ->
Iqtree.iqtree ~te:species_tree ~m:model ~st:(`CODON 1) (`phylip q)
|> Iqtree.treefile)
ali_files
|> List.zip_exn gene_ids
in
let gene_tree_set = RER.gene_tree_file gene_trees in
let phenotype = RER.phenotypes_of_convergent_species phenotypes in
......
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