library(ape)

tree <- read.tree("orignal.newick.tre") 
tree$node.label <- NULL 
tree$edge.length <- NULL
list=c(
        "p1440c63.2",
        "p8491c59.1",
        "p56091c35.1",
        "p238c64.56",
        "p2791c66.17",
        "p664c69.25",
        "p775c64.19",
        "p445c59.61",
        "p445c59.62",
        "p445c59.64",
        "Bgl_XP_013060646.1",
        "e4981c37.4",
        "e4981c37.5",
        "p445c59.58",
        "p445c59.54",
        "p445c59.46",
        "p238c64.61",
        "p664c69.13",
        "p1440c63.98",
        "p1440c63.90",
        "p1440c63.91",
        "p1440c63.103",
        "p665c65.65",
        "p1440c63.102",
        "p665c65.62",
        "X1XAF6",
        "p63233c38.1",
        "p3924c64.14",
        "p1412c61.2",
        "p30807c69.1",
        "p1440c63.76",
        "p1440c63.77",
        "p807c65.41",
        "p1440c63.73",
        "p1860c62.51",
        "p855c67.172",
        "p855c67.171",
        "p1440c63.58",
        "p807c65.22",
        "p807c65.25",
        "p1106c69.41",
        "p35389c41.1",
        "p19234c41.1",
        "p183713c35.1",
        "p59943c48.1",
        "p8162c67.89",
        "p3605c51.5",
        "e2244c39.16",
        "p30376c56.1",
        "e2244c39.20",
        "p665c65.48",
        "p8162c67.108",
        "p665c65.49",
        "p35754c38.1",
        "p3924c64.6",
        "p93400c36.1",
        "p254c66.117",
        "p3924c64.78",
        "p445c59.36",
        "p445c59.38",
        "p2057c61.46",
        "p266c63.161",
        "Bgl_XP_013072886.1",
        "p17174c35.1",
        "p737c53.70",
        "p1529c64.14"
         )

tree = drop.tip(tree, list)

write.tree(tree, file = "orignal.newick.mod.tre") # Save simplified_tree.txt


