tree = all_species_tree$scenario.3
plotTree(tree)
plotTreeTime(tree)
library(phytools)
tree = all_species_tree$scenario.3
plotTreeTime(tree)
plotTree(tree)
plotTree(tree, fsize = 0.2, lwd = 0.25)
plotTree(tree, fsize = 0.1, lwd = 0.25)
write.tree(tree, "~/Desktop/Figure.1a.tre")
specieslist <- read.csv("~/Desktop/Vphylomaker species_list.csv")
relative_tree <-  bind.relative(sp.list = specieslist, tree = GBOTB.extended, nodes=nodes.info.1)
tree.b <- phylo.maker(sp.list = relative_tree$species)
relative_tree <-  bind.relative(sp.list = specieslist, tree = GBOTB.extended, nodes=nodes.info.1)
relative_tree <-  bind.relative(sp.list = specieslist, tree = GBOTB.extended)
VPhyloMakerTree <- ape::read.tree("~/Desktop/Vphylomaker.tre")
MyTree <- ape::read.tree("~/Desktop/Concatenated_tree.tre")
VPhyloMakerTree <- compute.brlen(VPhyloMakerTree)
MyTree <- compute.brlen(MyTree)
MyTree <- ape::read.tree("~/Desktop/Concatenated_tree.tre")
VPhyloMakerTree <- compute.brlen(VPhyloMakerTree)
MyTree <- compute.brlen(MyTree)
assoc = cbind(MyTree$tip.label, MyTree$tip.label)
object <- cophylo(VPhyloMakerTree, MyTree, assoc = assoc, print = TRUE)
plot(object, lwd = 0.1, pts = 0.1, link.type = "curved", link.lwd = 0.5, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.1, rotate.multi = TRUE)
pdf(file = "~/Desktop/Compared_trees.pdf")
plot(object, lwd = 0.1, pts = 0.1, link.type = "curved", link.lwd = 0.5, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.1, rotate.multi = TRUE)
dev.off()
plot(object, lwd = 0.1, link.type = "curved", link.lwd = 0.5, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.05, rotate.multi = TRUE)
pdf(file = "~/Desktop/Compared_trees.pdf")
plot(object, lwd = 0.1, link.type = "curved", link.lwd = 0.5, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.05, rotate.multi = TRUE)
dev.off()
plot(object, lwd = 0.1, link.type = "curved", link.lwd = 0.5, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.05, rotate.multi = TRUE)
pdf(file = "~/Desktop/Compared_trees.pdf")
plot(object, lwd = 0.1, link.type = "curved", link.lwd = 0.5, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.05, rotate.multi = TRUE)
dev.off()
pdf(file = "~/Desktop/Compared_trees.pdf")
plot(object, lwd = 0.1, link.type = "curved", link.lwd = 0.5, link.lty = "solid", link.col = make.transparent("blue", 0.02), fsize = 0.01, rotate.multi = TRUE)
dev.off()
pdf(file = "~/Desktop/Compared_trees.pdf")
plot(object, lwd = 0.1, pts = 0.0001, link.type = "curved", link.lwd = 0.5, link.lty = "solid", link.col = make.transparent("blue", 0.02), fsize = 0.01, rotate.multi = TRUE)
dev.off()
plot(object, lwd = 0.1, pts = 0, link.type = "curved", link.lwd = 0.5, link.lty = "solid", link.col = make.transparent("blue", 0.02), fsize = 0.01, rotate.multi = TRUE)
plot(object, lwd = 0.1, pts = 0, link.type = "curved", link.lwd = 0.5, link.lty = "solid", link.col = make.transparent("blue", .02), fsize = 0.01, rotate.multi = TRUE)
pdf(file = "~/Desktop/Compared_trees.pdf")
plot(object, lwd = 0.1, pts = 0, link.type = "curved", link.lwd = 0.5, link.lty = "solid", link.col = make.transparent("blue", 0.02), fsize = 0.01, rotate.multi = TRUE)
dev.off()
plot(object, lwd = 0.1, pts = 0, link.type = "curved", link.lwd = 0.5, link.lty = "solid", link.col = make.transparent("blue", .02), fsize = 0.02, rotate.multi = TRUE)
pdf(file = "~/Desktop/Compared_trees.pdf")
plot(object, lwd = 0.1, pts = 0, link.type = "curved", link.lwd = 0.5, link.lty = "solid", link.col = make.transparent("blue", 0.02), fsize = 0.02, rotate.multi = TRUE)
dev.off()
pdf(file = "~/Desktop/Compared_trees.pdf")
plot(object, lwd = 0.1, pts = 0, link.type = "curved", link.lwd = 0.5, link.lty = "solid", link.col = make.transparent("blue", 0.01), fsize = 0.05, rotate.multi = TRUE)
dev.off()
library(ape)
library(phytools)
Gentianales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Gentianales/Gentianales.tre")
Gentianales_nuclear_tree <- ape::read.tree("~/Desktop/mrbayes/Gentianales/Gentianales_its2.tre")
Gentianales_chloroplast_tree <- compute.brlen(Gentianales_chloroplast_tree)
Gentianales_nuclear_tree <- compute.brlen(Gentianales_nuclear_tree)
Gentianales_chloroplast_tree <- midpoint_root(Gentianales_chloroplast_tree)
Gentianales_nuclear_tree <- midpoint.root(Gentianales_nuclear_tree)
Gentianales_association <- cbind(Gentianales_chloroplast_tree$tip.label, Gentianales_chloroplast_tree$tip.label)
obj <- cophylo(Gentianales_chloroplast_tree, Gentianales_nuclear_tree, assoc = Gentianales_association, print = TRUE)
plot(obj, lwd = 0.5, pts = 0.5, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.25, rotate.multi = TRUE)
plot(obj, lwd = 1, pts = 0.5, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.5, rotate.multi = TRUE)
plot(obj, lwd = 1, pts = 0.5, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.3, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Gentianales/Gentianales_comparison.pdf")
plot(obj, lwd = 1, pts = 0.5, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.3, rotate.multi = TRUE)
dev.off()
library(phytools)
Sapindales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Sapindales/Sapindales.tre")
Sapindales_nuclear_tree <- ape::read.tree("~/Desktop/mrbayes/Sapindales/Sapindales_its2.tre")
library(ape)
library(phytools)
Sapindales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Sapindales/Sapindales.tre")
Sapindales_nuclear_tree <- ape::read.tree("~/Desktop/mrbayes/Sapindales/Sapindales_its2.tre")
Sapindales_chloroplast_tree <- compute.brlen(Sapindales_chloroplast_tree)
Sapindales_nuclear_tree <- compute.brlen(Sapindales_nuclear_tree)
Sapindales_chloroplast_tree <- midpoint_root(Sapindales_chloroplast_tree)
Sapindales_nuclear_tree <- midpoint.root(Sapindales_nuclear_tree)
Sapindales_association <- cbind(Sapindales_chloroplast_tree$tip.label, Sapindales_chloroplast_tree$tip.label)
obj <- cophylo(Sapindales_chloroplast_tree, Sapindales_nuclear_tree, assoc = Sapindales_association, print = TRUE)
plot(obj, lwd = 1, pts = 0.5, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.3, rotate.multi = TRUE)
plot(obj, lwd = 1, pts = 0.2, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.1, rotate.multi = TRUE)
plot(obj, lwd = 1, pts = 0.2, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.2, rotate.multi = TRUE)
plot(obj, lwd = 1, pts = 0.2, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.2, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Sapindales/Sapindales_comparison.pdf")
plot(obj, lwd = 1, pts = 0.2, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.2, rotate.multi = TRUE)
dev.off()
plot(obj, pts = 0.2, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.2, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Sapindales/Sapindales_comparison.pdf")
plot(obj, pts = 0.2, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.2, rotate.multi = TRUE)
dev.off()
plot(obj, lwd = 1, pts = 0.2, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.25, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Sapindales/Sapindales_comparison.pdf")
plot(obj, lwd = 1, pts = 0.2, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.25, rotate.multi = TRUE)
dev.off()
library(phytools)
library(ape)
library(phytools)
Arecales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Arecales/Arecales.tre")
Arecales_nuclear_tree <- ape::read.tree("~/Desktop/mrbayes/Arecales/Arecales_its2.tre")
Arecales_chloroplast_tree <- compute.brlen(Arecales_chloroplast_tree)
Arecales_nuclear_tree <- compute.brlen(Arecales_nuclear_tree)
Arecales_chloroplast_tree <- midpoint_root(Arecales_chloroplast_tree)
Arecales_nuclear_tree <- midpoint.root(Arecales_nuclear_tree)
Arecales_association <- cbind(Arecales_chloroplast_tree$tip.label, Arecales_chloroplast_tree$tip.label)
obj <- cophylo(Arecales_chloroplast_tree, Arecales_nuclear_tree, assoc = Arecales_association, print = TRUE)
plot(obj, lwd = 1.5, pts = 0.3, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.7, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Arecales/Arecales_comparison.pdf")
plot(obj, lwd = 1.5, pts = 0.3, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.7, rotate.multi = TRUE)
dev.off()
Arecales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Arecales/Arecales.tre")
Arecales_nuclear_tree <- ape::read.tree("~/Desktop/mrbayes/Arecales/Arecales_its2.tre")
Arecales_chloroplast_tree <- compute.brlen(Arecales_chloroplast_tree)
Arecales_nuclear_tree <- compute.brlen(Arecales_nuclear_tree)
Arecales_association <- cbind(Arecales_chloroplast_tree$tip.label, Arecales_chloroplast_tree$tip.label)
obj <- cophylo(Arecales_chloroplast_tree, Arecales_nuclear_tree, assoc = Arecales_association, print = TRUE)
plot(obj, lwd = 1.5, pts = 0.3, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.7, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Arecales/Arecales_comparison.pdf")
plot(obj, lwd = 1.5, pts = 0.3, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.7, rotate.multi = TRUE)
dev.off()
Arecales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Arecales/Arecales.tre")
Arecales_nuclear_tree <- ape::read.tree("~/Desktop/mrbayes/Arecales/Arecales_its2.tre")
Arecales_chloroplast_tree <- compute.brlen(Arecales_chloroplast_tree)
Arecales_nuclear_tree <- compute.brlen(Arecales_nuclear_tree)
Arecales_chloroplast_tree <- midpoint_root(Arecales_chloroplast_tree)
Arecales_nuclear_tree <- midpoint.root(Arecales_nuclear_tree)
Arecales_association <- cbind(Arecales_chloroplast_tree$tip.label, Arecales_chloroplast_tree$tip.label)
obj <- cophylo(Arecales_chloroplast_tree, Arecales_nuclear_tree, assoc = Arecales_association, print = TRUE)
plot(obj, lwd = 1.5, pts = 0.3, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.7, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Arecales/Arecales_comparison.pdf")
plot(obj, lwd = 1.5, pts = 0.3, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.7, rotate.multi = TRUE)
dev.off()
plot(obj, lwd = 1.5, pts = 0.5, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.7, rotate.multi = TRUE)
plot(obj, lwd = 1.5, pts = 1, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.7, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Arecales/Arecales_comparison.pdf")
plot(obj, lwd = 1.5, pts = 1, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.7, rotate.multi = TRUE)
dev.off()
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE)
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 1, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE)
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.7, rotate.multi = TRUE)
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Arecales/Arecales_comparison.pdf")
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE)
dev.off()
library(ape)
library(phytools)
Asterales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Asterales/Asterales.tre")
Asterales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Asterales/Asterales.tre")
Asterales_nuclear_tree <- ape::read.tree("~/Desktop/mrbayes/Asterales/Asterales_its2.tre")
Asterales_chloroplast_tree <- compute.brlen(Asterales_chloroplast_tree)
Asterales_nuclear_tree <- compute.brlen(Asterales_nuclear_tree)
Asterales_chloroplast_tree <- midpoint_root(Asterales_chloroplast_tree)
Asterales_nuclear_tree <- midpoint.root(Asterales_nuclear_tree)
Asterales_association <- cbind(Asterales_chloroplast_tree$tip.label, Asterales_chloroplast_tree$tip.label)
obj <- cophylo(Asterales_chloroplast_tree, Asterales_nuclear_tree, assoc = Asterales_association, print = TRUE)
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Asterales/Asterales_comparison.pdf")
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE)
dev.off()
library(dplyr)
chloroplast_specieslist <- read.csv("~/Desktop/mrbayes/chloroplast_specieslist.csv")
all_specieslist <- read.csv("/Desktop/final_dataset.csv")
all_specieslist <- read.csv("/Desktop/final_dataset,csv")
library(readr)
all_specieslist <- read_csv("Desktop/final_dataset.csv")
View(all_specieslist)
all_specieslist <- read_csv("Desktop/final_dataset.csv")
chloroplast_specieslist <- read.csv("~/Desktop/mrbayes/chloroplast_specieslist.csv", header = TRUE)
all_specieslist <- read_csv("Desktop/final_dataset.csv", header = TRUE)
for_vphylomaker <- inner_join(all_specieslist, chloroplast_specieslist, by ="speciesnames")
for_vphylomaker <- inner_join(all_specieslist, chloroplast_specieslist)
chloroplast_specieslist <- read.csv("~/Desktop/mrbayes/chloroplast_specieslist.csv", header = TRUE)
all_specieslist <- read_csv("Desktop/final_dataset.csv")
for_vphylomaker <- inner_join(all_specieslist, chloroplast_specieslist)
for_vphylomaker <- inner_join(all_specieslist, chloroplast_specieslist, by = "speciesnames")
View(for_vphylomaker)
write.csv(for_vphylomaker, "~/Desktop/for_vphylomaker.csv")
knitr::opts_chunk$set(echo = TRUE)
# Opening the Pacakages for use
library(ape)
library(V.PhyloMaker)
all_species_tree <-  phylo.maker(sp.list = for_vphylomaker, tree = GBOTB.extended, nodes=nodes.info.1, scenarios="S3")
all_species_tree <-  phylo.maker(sp.list = for_vphylomaker, tree = GBOTB.extended, nodes=nodes.info.1, scenarios="S3")
write.tree(all_species_tree$scenario.3, "Figure.1a.tre")
write.tree(all_species_tree$scenario.3, "~/Desktop/Figure.1a.tre")
chloroplast_tree <- ape::read.tree("~/Desktop/concatenated_tree.tre")
vphylomaker_tree <- ape:read.tree("~/Desktop/vphylomaker_chloroplast_tree.tre")
vphylomaker_tree <- read.tree("~/Desktop/vphylomaker_chloroplast_tree.tre")
library(ape)
library(phytools)
chloroplast_tree <- ape::read.tree("~/Desktop/concatenated_tree.tre")
vphylomaker_tree <- ape:read.tree("~/Desktop/vphylomaker_chloroplast_tree.tre")
vphylomaker_tree <- ape::read.tree("~/Desktop/vphylomaker_chloroplast_tree.tre")
comparePhylo(chloroplast_tree, vphylomaker_tree, plot = TRUE, use.edge.length = TRUE)
comparePhylo(chloroplast_tree, vphylomaker_tree, plot = TRUE)
chloroplast_tree <- compute.brlen(chloroplast_tree)
chloroplast_tree <- ape::read.tree("~/Desktop/concatenated_tree.tre")
vphylomaker_tree <- ape::read.tree("~/Desktop/vphylomaker_chloroplast_tree.tre")
chloroplast_tree <- compute.brlen(chloroplast_tree)
vphylomaker_tree <- compute.brlen(vphylomaker_tree)
comparePhylo(chloroplast_tree, vphylomaker_tree, plot = TRUE)
chloroplast_tree <- ape::read.tree("~/Desktop/concatenated_tree.tre")
vphylomaker_tree <- ape::read.tree("~/Desktop/vphylomaker_chloroplast_tree.tre")
chloroplast_tree <- compute.brlen(chloroplast_tree)
vphylomaker_tree <- compute.brlen(vphylomaker_tree)
comparePhylo(chloroplast_tree, vphylomaker_tree, plot = TRUE)
chloroplast_tree <- ape::read.tree("~/Desktop/concatenated_tree.tre")
vphylomaker_tree <- ape::read.tree("~/Desktop/vphylomaker.tre")
chloroplast_tree <- ape::read.tree("~/Desktop/concatenated_tree.tre")
vphylomaker_tree <- ape::read.tree("~/Desktop/vphylomaker.tre")
chloroplast_tree <- compute.brlen(chloroplast_tree)
vphylomaker_tree <- compute.brlen(vphylomaker_tree)
comparePhylo(chloroplast_tree, vphylomaker_tree, plot = TRUE)
ed.calc(vphylomaker_tree)
install.packages("PDcalc")
library(pdcalc)
library(PDcalc)
devtools::install_github("davidnipperess/PDcalc",build_vignettes = TRUE)
obj <- cophylo(Asterales_chloroplast_tree, Asterales_nuclear_tree, assoc = Asterales_association, print = TRUE, nodelabels = "prob")
library(ape)
library(phytools)
Asterales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Asterales/Asterales.tre")
Asterales_nuclear_tree <- ape::read.tree("~/Desktop/mrbayes/Asterales/Asterales_its2.tre")
Asterales_chloroplast_tree <- compute.brlen(Asterales_chloroplast_tree)
Asterales_nuclear_tree <- compute.brlen(Asterales_nuclear_tree)
Asterales_chloroplast_tree <- midpoint_root(Asterales_chloroplast_tree)
Asterales_nuclear_tree <- midpoint.root(Asterales_nuclear_tree)
Asterales_association <- cbind(Asterales_chloroplast_tree$tip.label, Asterales_chloroplast_tree$tip.label)
obj <- cophylo(Asterales_chloroplast_tree, Asterales_nuclear_tree, assoc = Asterales_association, print = TRUE, nodelabels = "prob")
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE)
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE, nodelabels = "prob")
Asterales_association <- cbind(Asterales_chloroplast_tree$tip.label, Asterales_chloroplast_tree$tip.label)
obj <- cophylo(Asterales_chloroplast_tree, Asterales_nuclear_tree, assoc = Asterales_association, print = TRUE )
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE, nodelabels = "prob")
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE, node.numbers=TRUE)
obj <- cophylo(Asterales_chloroplast_tree, Asterales_nuclear_tree, assoc = Asterales_association, print = TRUE )
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE, node.numbers=TRUE)
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE, node.numbers=TRUE)
pdf(file = "~/Desktop/mrbayes/Asterales/Asterales_comparison.pdf")
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE, node.numbers=TRUE)
dev.off()
chloroplast_tree <- ape::read.tree("~/Desktop/concatenated_tree.tre")
vphylomaker_tree <- ape::read.tree("~/Desktop/vphylomaker.tre")
nodelabels.cophylo(obj,  which=c("left","right"))
nodelabels.cophylo(obj)
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE, node.numbers=TRUE)
nodelabels.cophylo(obj)
edgelabels(obj, which = c('left', 'right'))
edgelabels(obj$node.label, which = c('left', 'right'))
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE, node.numbers=TRUE)
edgelabels(obj$node.label, which = c('left', 'right'))
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE, node.numbers=TRUE)
Asparagales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Asparaagales/Asparaagales.tre")
Asparagales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Asparaagales/Asparaagales.tre")
library(ape)
library(phytools)
Asparagales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Asparaagales/Asparaagales.tre")
Asparagales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Asparagales/Asparagales.tre")
Asparagales_chloroplast_tree <- compute.brlen(Asparagales_chloroplast_tree)
obj <- cophylo(Asparagales_chloroplast_tree, Asparagales_nuclear_tree, assoc = Asparagales_association, print = TRUE)
plot(Asparagales_chloroplast_tree, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE)
knitr::opts_chunk$set(echo = TRUE)
# Opening the Pacakages for use
library(ape)
knitr::opts_chunk$set(echo = TRUE)
library(V.PhyloMaker)
specieslist <- read.csv("~/Desktop/malpighiales_vphylo.csv")
relative_tree <-  bind.relative(sp.list = specieslist, tree = GBOTB.extended, nodes=nodes.info.1)
tree.b <- phylo.maker(sp.list = relative_tree$species)
specieslist <- read.csv("~/Desktop/malpighiales_vphylo.csv")
relative_tree <-  bind.relative(sp.list = specieslist, tree = GBOTB.extended, nodes=nodes.info.1)
for_vphylomaker <- read.csv("~/Desktop/malpighiales_vphylo.csv")
all_species_tree <-  phylo.maker(sp.list = for_vphylomaker, tree = GBOTB.extended, nodes=nodes.info.1, scenarios="S3")
all_species_tree <-  phylo.maker(sp.list = for_vphylomaker, tree = GBOTB.extended, nodes=nodes.info.1, scenarios="S3")
write.tree(all_species_tree$scenario.3, "~/Desktop/Figure.1a.tre")
Malpighiales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Malpighiales/malpighiales.tre")
Malpighiales_nuclear_tree <- ape::read.tree("~/Desktop/mrbayes/Malpighiales/malpighiales_v.tre")
Malpighiales_chloroplast_tree <- compute.brlen(Malpighiales_chloroplast_tree)
Malpighiales_nuclear_tree <- compute.brlen(Malpighiales_nuclear_tree)
Malpighiales_chloroplast_tree <- midpoint_root(Malpighiales_chloroplast_tree)
library(ape)
library(phytools)
Malpighiales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Malpighiales/malpighiales.tre")
Malpighiales_nuclear_tree <- ape::read.tree("~/Desktop/mrbayes/Malpighiales/malpighiales_v.tre")
Malpighiales_chloroplast_tree <- compute.brlen(Malpighiales_chloroplast_tree)
Malpighiales_nuclear_tree <- compute.brlen(Malpighiales_nuclear_tree)
Malpighiales_association <- cbind(Malpighiales_chloroplast_tree$tip.label, Malpighiales_chloroplast_tree$tip.label)
obj <- cophylo(Malpighiales_chloroplast_tree, Malpighiales_nuclear_tree, assoc = Malpighiales_association, print = TRUE)
plot(Malpighiales_chloroplast_tree, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE)
plot(obj, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE)
plot(obj, lwd = 1, pts = 0.3, link.type = "curved", link.lwd = 0.2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.02, rotate.multi = TRUE)
plot(obj, lwd = 1, pts = 0.3, link.type = "curved", link.lwd = 0.2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.2, rotate.multi = TRUE)
plot(obj, lwd = 1, pts = 0.3, link.type = "curved", link.lwd = 0.2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.2, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Malpighiales/Malpighiales_comparison.pdf")
plot(obj, lwd = 1, pts = 0.3, link.type = "curved", link.lwd = 0.2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.2, rotate.multi = TRUE)
dev.off()
chloroplast_tree <- ape::read.tree("~/Desktop/concatenated_tree.tre")
vphylomaker_tree <- ape::read.tree("~/Desktop/vphylomaker.tre")
Malpighiales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Malpighiales/malpighiales_its2.tre")
Malpighiales_nuclear_tree <- ape::read.tree("~/Desktop/mrbayes/Malpighiales/malpighiales_v.tre")
Malpighiales_chloroplast_tree <- compute.brlen(Malpighiales_chloroplast_tree)
Malpighiales_nuclear_tree <- compute.brlen(Malpighiales_nuclear_tree)
Malpighiales_chloroplast_tree <- midpoint_root(Malpighiales_chloroplast_tree)
Malpighiales_nuclear_tree <- midpoint.root(Malpighiales_nuclear_tree)
Malpighiales_association <- cbind(Malpighiales_chloroplast_tree$tip.label, Malpighiales_chloroplast_tree$tip.label)
obj <- cophylo(Malpighiales_chloroplast_tree, Malpighiales_nuclear_tree, assoc = Malpighiales_association, print = TRUE)
plot(obj, lwd = 1, pts = 0.3, link.type = "curved", link.lwd = 0.2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.2, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Malpighiales/Malpighiales_comparison.pdf")
plot(obj, lwd = 1, pts = 0.3, link.type = "curved", link.lwd = 0.2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.2, rotate.multi = TRUE)
dev.off()
chloroplast_tree <- ape::read.tree("~/Desktop/concatenated_tree.tre")
vphylomaker_tree <- ape::read.tree("~/Desktop/vphylomaker.tre")
plot(obj, lwd = 0.5, pts = 0.3, link.type = "curved", link.lwd = 0.3, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.3, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Malpighiales/Malpighiales_comparison.pdf")
plot(obj, lwd = 0.5, pts = 0.3, link.type = "curved", link.lwd = 0.3, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.3, rotate.multi = TRUE)
dev.off()
chloroplast_tree <- ape::read.tree("~/Desktop/concatenated_tree.tre")
Malpighiales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Malpighiales/malpighiales.tre")
Malpighiales_nuclear_tree <- ape::read.tree("~/Desktop/mrbayes/Malpighiales/malpighiales_v.tre")
Malpighiales_chloroplast_tree <- compute.brlen(Malpighiales_chloroplast_tree)
Malpighiales_nuclear_tree <- compute.brlen(Malpighiales_nuclear_tree)
Malpighiales_chloroplast_tree <- midpoint_root(Malpighiales_chloroplast_tree)
Malpighiales_nuclear_tree <- midpoint.root(Malpighiales_nuclear_tree)
Malpighiales_association <- cbind(Malpighiales_chloroplast_tree$tip.label, Malpighiales_chloroplast_tree$tip.label)
obj <- cophylo(Malpighiales_chloroplast_tree, Malpighiales_nuclear_tree, assoc = Malpighiales_association, print = TRUE)
plot(obj, lwd = 0.5, pts = 0.3, link.type = "curved", link.lwd = 0.3, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.3, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Malpighiales/Malpighiales_comparison.pdf")
plot(obj, lwd = 0.5, pts = 0.3, link.type = "curved", link.lwd = 0.3, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.3, rotate.multi = TRUE)
dev.off()
chloroplast_tree <- ape::read.tree("~/Desktop/concatenated_tree.tre")
vphylomaker_tree <- ape::read.tree("~/Desktop/vphylomaker.tre")
chloroplast_tree <- compute.brlen(chloroplast_tree)
for_vphylomaker <- read.csv("~/Desktop/malpighiales_vphylo.csv")
all_species_tree <-  phylo.maker(sp.list = for_vphylomaker, tree = GBOTB.extended, nodes=nodes.info.1, scenarios="S3")
all_species_tree <-  phylo.maker(sp.list = for_vphylomaker, tree = GBOTB.extended, nodes=nodes.info.1, scenarios="S3")
write.tree(all_species_tree$scenario.3, "~/Desktop/Figure.1a.tre")
library(ape)
library(phytools)
Malpighiales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Malpighiales/malpighiales.tre")
Malpighiales_nuclear_tree <- ape::read.tree("~/Desktop/mrbayes/Malpighiales/malpighiales_v.tre")
Malpighiales_chloroplast_tree <- compute.brlen(Malpighiales_chloroplast_tree)
Malpighiales_nuclear_tree <- compute.brlen(Malpighiales_nuclear_tree)
Malpighiales_chloroplast_tree <- midpoint_root(Malpighiales_chloroplast_tree)
Malpighiales_nuclear_tree <- midpoint.root(Malpighiales_nuclear_tree)
Malpighiales_association <- cbind(Malpighiales_chloroplast_tree$tip.label, Malpighiales_chloroplast_tree$tip.label)
obj <- cophylo(Malpighiales_chloroplast_tree, Malpighiales_nuclear_tree, assoc = Malpighiales_association, print = TRUE)
plot(obj, lwd = 0.5, pts = 0.3, link.type = "curved", link.lwd = 0.3, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.3, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Malpighiales/Malpighiales_comparison_cpDNA_V.pdf")
plot(obj, lwd = 0.5, pts = 0.3, link.type = "curved", link.lwd = 0.3, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.3, rotate.multi = TRUE)
dev.off()
Malpighiales_chloroplast_tree <- ape::read.tree("~/Desktop/mrbayes/Malpighiales/malpighiales_its2.tre")
Malpighiales_nuclear_tree <- ape::read.tree("~/Desktop/mrbayes/Malpighiales/malpighiales_v.tre")
Malpighiales_chloroplast_tree <- compute.brlen(Malpighiales_chloroplast_tree)
Malpighiales_nuclear_tree <- compute.brlen(Malpighiales_nuclear_tree)
Malpighiales_chloroplast_tree <- midpoint_root(Malpighiales_chloroplast_tree)
Malpighiales_nuclear_tree <- midpoint.root(Malpighiales_nuclear_tree)
Malpighiales_association <- cbind(Malpighiales_chloroplast_tree$tip.label, Malpighiales_chloroplast_tree$tip.label)
obj <- cophylo(Malpighiales_chloroplast_tree, Malpighiales_nuclear_tree, assoc = Malpighiales_association, print = TRUE)
plot(obj, lwd = 0.5, pts = 0.3, link.type = "curved", link.lwd = 0.3, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.3, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Malpighiales/Malpighiales_comparison_its2_v.pdf")
plot(obj, lwd = 0.5, pts = 0.3, link.type = "curved", link.lwd = 0.3, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 0.3, rotate.multi = TRUE)
dev.off()
install.packages("GEIGER")
yes
y
install.packages("geiger")
library(geiger)
congruify.phylo(reference = "~/Desktop/Manuscript/mrbayes/VPhylomaker.tre", target = "~/Desktop/Manuscript/Data Availability Section/Concatenated_tree.tre")
ref_tree <- read.tree("~/Desktop/Manuscript/mrbayes/VPhylomaker.tre")
target_tree <- read.tree("~/Desktop/Manuscript/Data Availability Section/Concatenated_tree.tre")
class(ref_tree)  # Should return "phylo"
class(target_tree)  # Should return "phylo"
congruity.phylo(list(ref_tree, target_tree))
congruify.phylo(list(ref_tree, target_tree))
congruify.phylo(reference = ref_tree, target = target_tree)
new_tree <- congruify.phylo(reference = ref_tree, target = target_tree)
lot.phylo(ref_tree)
plot.phylo(ref_tree)
plot.phylo(target_tree)
is.rooted(ref_tree)
is.rooted(target_tree)
plot.phylo(new_)
plot.phylo(new_tree)
rooted_target_tree <- root(target_tree, outgroup = "physcomitrella_patens", resolve.root = TRUE)
rooted_target_tree <- root(target_tree, outgroup = "Physcomitrella_patens", resolve.root = TRUE)
new_tree <- congruify.phylo(reference = ref_tree, target = rooted_target_tree)
ultrametric_ref_tree <- force.ultrametric(ref_tree, method = "extend")
new_tree <- congruify.phylo(reference = ref_tree, target = rooted_target_tree)
load("~/.RData")
# reading sequences from file
setwd(dir ="/Users/amrit/Desktop/arecales")
arecales_matk_num <-read.csv("arecales_matk.csv")
arecales_matk <- read.GenBank(arecales_matk_num$matk)
#install.packages("seqinr")
#install.packages("ape")
# install.packages("tidyverse")
# install.packages("readxl")
library(seqinr)
library(ape)
# library(dplyr)
library(tidyverse)
install.packages("xlsx")
library(xlsx)
#install.packages("seqinr")
#install.packages("ape")
# install.packages("tidyverse")
# install.packages("readxl")
library(seqinr)
library(ape)
# library(dplyr)
library(tidyverse)
install.packages("xlsx")
library(xlsx)
arecales_matk <- read.GenBank(arecales_matk_num$matk)
install.packages("seqinr")
install.packages("ape")
install.packages("tidyverse")
install.packages("readxl")
library(seqinr)
library(ape)
library(dplyr)
library(tidyverse)
install.packages("xlsx")
library(xlsx)
# reading sequences from file
setwd(dir ="/Users/amrit/Desktop/arecales")
arecales_matk_num <-read.csv("arecales_matk.csv")
arecales_matk <- read.GenBank(arecales_matk_num$matk)
library(ape)
arecales_matk <- read.GenBank(arecales_matk_num$matk)
arecales_trnh_num <- read.csv("arecales_trnh.csv")
arecales_trnh <- read.GenBank(arecales_trnh_num$trnh_psba)
its1_num <- read.csv("arecales_its2.csv")
its1_num <- read.csv("arecales_its1.csv")
its1 <- read.GenBank(its1_num$its)
its2_num <- read.csv("arecales_its2.csv")
its2 <- read.GenBank(its2_num$its2)
its1_num <- read.csv("arecales_its1.csv")
its1 <- read.GenBank(its1_num$its)
its1_IDs <- paste(attr(its1, "species"), names(its1), sep = "_its1_")
its2_IDs <- paste(attr(its2, "species"), names(its2), sep = "_its2_")
its1_IDs
its2_IDs
write.dna(its1, file = "its1.fasta", format = "fasta", append = FALSE)
write.dna(its2, file = "its2.fasta", format = "fasta", append = FALSE)
its1_seqinr <- read.fasta(file = "its1.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
its2_seqinr <- read.fasta(file = "its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = its1_seqinr, names = its1_IDs, file.out = "its1_sequences.fasta")
write.fasta(sequences = its2_seqinr, names = its2_IDs, file.out = "its2_sequences.fasta")
library(ape)
library(seqinr)
library(dplyr)
write.dna(its1, file = "its1.fasta", format = "fasta", append = FALSE)
write.dna(its2, file = "its2.fasta", format = "fasta", append = FALSE)
its1_seqinr <- read.fasta(file = "its1.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
its2_seqinr <- read.fasta(file = "its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = its1_seqinr, names = its1_IDs, file.out = "its1_sequences.fasta")
write.fasta(sequences = its2_seqinr, names = its2_IDs, file.out = "its2_sequences.fasta")
arecales_matk_num <-read.csv("arecales_matk.csv")
arecales_matk <- read.GenBank(arecales_matk_num$matk)
arecales_rbcL_num <- read.csv("arecales_rbcl.csv")
arecales_rbcL <- read.GenBank(arecales_rbcL_num$rbcL)
arecales_trnh_num <- read.csv("arecales_trnh.csv")
arecales_trnh <- read.GenBank(arecales_trnh_num$trnh_psba)
its1_num <- read.csv("arecales_its1.csv")
its1 <- read.GenBank(its1_num$its)
its2_num <- read.csv("arecales_its2.csv")
its2 <- read.GenBank(its2_num$its2)
write.dna(its2, file = "its2.fasta", format = "fasta", append = FALSE)
its2_seqinr <- read.fasta(file = "its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = its2_seqinr, names = its2_num$speciesnames, file.out = "its2_sequences.fasta")
library(ape)
library(phytools)
library(ape)
library(phytools)
Arecales_chloroplast_tree <- ape::read.tree("~/Desktop/Arecales/Arecales.tre")
Arecales_nuclear_tree <- ape::read.tree("~/Desktop/Arecales/Arecales_its2.tre")
Arecales_chloroplast_tree <- compute.brlen(Arecales_chloroplast_tree)
Arecales_nuclear_tree <- compute.brlen(Arecales_nuclear_tree)
Arecales_chloroplast_tree <- ape::read.tree("~/Desktop/Arecales/Arecales.tre")
Arecales_nuclear_tree <- ape::read.tree("~/Desktop/Arecales/Arecales_its2.tre")
Arecales_chloroplast_tree <- compute.brlen(Arecales_chloroplast_tree)
Arecales_nuclear_tree <- compute.brlen(Arecales_nuclear_tree)
Arecales_nuclear_tree <- ape::read.tree("~/Desktop/Arecales/Arecales_its2.tre")
Arecales_chloroplast_tree <- compute.brlen(Arecales_chloroplast_tree)
Arecales_nuclear_tree <- compute.brlen(Arecales_nuclear_tree)
Arecales_chloroplast_tree <- midpoint_root(Arecales_chloroplast_tree)
Arecales_nuclear_tree <- midpoint.root(Arecales_nuclear_tree)
Arecales_association <- cbind(Arecales_chloroplast_tree$tip.label, Arecales_chloroplast_tree$tip.label)
obj <- cophylo(Arecales_chloroplast_tree, Arecales_nuclear_tree, assoc = Arecales_association, print = TRUE)
plot(Arecales_chloroplast_tree, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE)
Arecales_chloroplast_tree <- midpoint_root(Arecales_chloroplast_tree)
Arecales_nuclear_tree <- midpoint.root(Arecales_nuclear_tree)
Arecales_association <- cbind(Arecales_chloroplast_tree$tip.label, Arecales_chloroplast_tree$tip.label)
obj <- cophylo(Arecales_chloroplast_tree, Arecales_nuclear_tree, assoc = Arecales_association, print = TRUE)
plot(Arecales_chloroplast_tree, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE)
pdf(file = "~/Desktop/mrbayes/Arecales/Arecales_comparison.pdf")
Arecales_chloroplast_tree <- midpoint_root(Arecales_chloroplast_tree)
Arecales_nuclear_tree <- midpoint.root(Arecales_nuclear_tree)
Arecales_chloroplast_tree <- ape::read.tree("~/Desktop/Arecales/Arecales.tre")
Arecales_nuclear_tree <- ape::read.tree("~/Desktop/Arecales/Arecales_its2.tre")
Arecales_chloroplast_tree <- compute.brlen(Arecales_chloroplast_tree)
Arecales_nuclear_tree <- compute.brlen(Arecales_nuclear_tree)
Arecales_chloroplast_tree <- midpoint_root(Arecales_chloroplast_tree)
Arecales_nuclear_tree <- midpoint.root(Arecales_nuclear_tree)
Arecales_association <- cbind(Arecales_chloroplast_tree$tip.label, Arecales_chloroplast_tree$tip.label)
obj <- cophylo(Arecales_chloroplast_tree, Arecales_nuclear_tree, assoc = Arecales_association, print = TRUE)
plot(Arecales_chloroplast_tree, lwd = 2, pts = 1, link.type = "curved", link.lwd = 2, link.lty = "solid", link.col = make.transparent("blue", .25), fsize = 1, rotate.multi = TRUE)
Arecales_association <- cbind(Arecales_chloroplast_tree$tip.label, Arecales_chloroplast_tree$tip.label)
