library(ape)
tree <- read.tree("orignal.newick.tre")
tree$node.label <- NULL
tree$edge.length <- NULL
tree = drop.tip(tree, "X1XAF6")
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",
"Acl_XP_012941580.1",
"p35389c41.1",
"p19234c41.1",
"p183713c35.1",
"p59943c48.1",
"p8162c67.89",
"p3605c51.5",
"e2244c39.16",
"p30376c56.1",
"Acl_XP_005104863.1",
"e2244c39.20",
"p665c65.48",
"p8162c67.108",
"p665c65.49",
"p35754c38.1",
"Acl_XP_005098204.2",
"p3924c64.6",
"p93400c36.1",
"p254c66.117",
"p3924c64.78",
"p445c59.36",
"p445c59.38",
"Acl_XP_012937308.1",
"p2057c61.46",
"p266c63.161",
"Bgl_XP_013072886.1",
"p17174c35.1",
"p737c53.70",
"Acl_XP_012941581.1",
"p1529c64.14")
tree = drop.tip(tree, list)
write.tree(tree, file = "orignal.newick.mod.tre") # Save simplified_tree.txt
