install.packages("ape")
install.packags("seqinr")
install.packages("seqinr")
library("seqinr")
library(ape)
library(seqinr)
library(ape)
setwd(dir ="~/Desktop/mrbayes/Myrtales")
Arecales_its1 <- read.csv("Arecales_its1.csv")
setwd(dir ="~/Desktop/mrbayes/Arecales")
Arecales_its1 <- read.csv("Arecales_its1.csv")
Arecales_its1_genbank_its1 <- read.GenBank(Arecales_its1$its1)
write.dna(Arecales_its1_genbank_its1, file = "Arecales_its1.fasta", format = "fasta", append = FALSE)
Arecales_its1_seqinr <- read.fasta(file = "Arecales_its1.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Arecales_its1_seqinr, names = Arecales_its1$speciesname, file.out = "Arecales_its1_sequences.fasta")
Arecales_its2 <- read.csv("Arecales_its2.csv")
Arecales_its2_genbank_its2 <- read.GenBank(Arecales_its2$its2)
write.dna(Arecales_its2_genbank_its2, file = "Arecales_its2.fasta", format = "fasta", append = FALSE)
Arecales_its2_seqinr <- read.fasta(file = "Arecales_its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Arecales_its2_seqinr, names = Arecales_its2$speciesname, file.out = "Arecales_its2_sequences.fasta")
setwd(dir ="~/Desktop/mrbayes/Asparagales")
Asparagales_its1 <- read.csv("Asparagales_its1.csv")
Asparagales_its1_genbank_its1 <- read.GenBank(Asparagales_its1$its1)
write.dna(Asparagales_its1_genbank_its1, file = "Asparagales_its1.fasta", format = "fasta", append = FALSE)
Asparagales_its1_seqinr <- read.fasta(file = "Asparagales_its1.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Asparagales_its1_seqinr, names = Asparagales_its1$speciesname, file.out = "Asparagales_its1_sequences.fasta")
Asparagales_its2 <- read.csv("Asparagales_its2.csv")
Asparagales_its2_genbank_its2 <- read.GenBank(Asparagales_its2$its2)
write.dna(Asparagales_its2_genbank_its2, file = "Asparagales_its2.fasta", format = "fasta", append = FALSE)
Asparagales_its2_seqinr <- read.fasta(file = "Asparagales_its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Asparagales_its2_seqinr, names = Asparagales_its2$speciesname, file.out = "Asparagales_its2_sequences.fasta")
setwd(dir ="~/Desktop/mrbayes/Aquifoliales")
Aquifoliales_rbcL <- read.csv("Aquifoliales_rbcL.csv")
setwd(dir ="~/Desktop/mrbayes/Aquifoliales")
Aquifoliales_its1 <- read.csv("Aquifoliales_its1.csv")
Aquifoliales_its2 <- read.csv("Aquifoliales_its2.csv")
Aquifoliales_its2_genbank_its2 <- read.GenBank(Aquifoliales_its2$its2)
write.dna(Aquifoliales_its2_genbank_its2, file = "Aquifoliales_its2.fasta", format = "fasta", append = FALSE)
Aquifoliales_its2_seqinr <- read.fasta(file = "Aquifoliales_its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Aquifoliales_its2_seqinr, names = Aquifoliales_its2$speciesname, file.out = "Aquifoliales_its2_sequences.fasta")
setwd(dir ="~/Desktop/mrbayes/Arecales")
Arecales_its1 <- read.csv("Arecales_its1.csv")
Arecales_its1_genbank_its1 <- read.GenBank(Arecales_its1$its1)
write.dna(Arecales_its1_genbank_its1, file = "Arecales_its1.fasta", format = "fasta", append = FALSE)
Arecales_its1_seqinr <- read.fasta(file = "Arecales_its1.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Arecales_its1_seqinr, names = Arecales_its1$speciesname, file.out = "Arecales_its1_sequences.fasta")
Arecales_its2 <- read.csv("Arecales_its2.csv")
Arecales_its2_genbank_its2 <- read.GenBank(Arecales_its2$its2)
write.dna(Arecales_its2_genbank_its2, file = "Arecales_its2.fasta", format = "fasta", append = FALSE)
Arecales_its2_seqinr <- read.fasta(file = "Arecales_its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Arecales_its2_seqinr, names = Arecales_its2$speciesname, file.out = "Arecales_its2_sequences.fasta")
setwd(dir ="~/Desktop/mrbayes/Asparagales")
Asparagales_its1 <- read.csv("Asparagales_its1.csv")
setwd(dir ="~/Desktop/mrbayes/Asparagales")
Asparagales_its2 <- read.csv("Asparagales_its2.csv")
Asparagales_its2_genbank_its2 <- read.GenBank(Asparagales_its2$its2)
write.dna(Asparagales_its2_genbank_its2, file = "Asparagales_its2.fasta", format = "fasta", append = FALSE)
Asparagales_its2_seqinr <- read.fasta(file = "Asparagales_its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Asparagales_its2_seqinr, names = Asparagales_its2$speciesname, file.out = "Asparagales_its2_sequences.fasta")
setwd(dir ="~/Desktop/mrbayes/Asterales")
Asterales_its1 <- read.csv("Asterales_its1.csv")
Asterales_its1_genbank_its1 <- read.GenBank(Asterales_its1$its1)
Asterales_its2 <- read.csv("Asterales_its2.csv")
Asterales_its2_genbank_its2 <- read.GenBank(Asterales_its2$its2)
write.dna(Asterales_its2_genbank_its2, file = "Asterales_its2.fasta", format = "fasta", append = FALSE)
Asterales_its2_seqinr <- read.fasta(file = "Asterales_its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Asterales_its2_seqinr, names = Asterales_its2$speciesname, file.out = "Asterales_its2_sequences.fasta")
setwd(dir ="~/Desktop/mrbayes/Boraginales")
Boraginales_its1 <- read.csv("Boraginales_its1.csv")
Boraginales_its2 <- read.csv("Boraginales_its2.csv")
Boraginales_its2_genbank_its2 <- read.GenBank(Boraginales_its2$its2)
write.dna(Boraginales_its2_genbank_its2, file = "Boraginales_its2.fasta", format = "fasta", append = FALSE)
setwd(dir ="~/Desktop/mrbayes/Boraginales")
Boraginales_its2 <- read.csv("Boraginales_its2.csv")
Boraginales_its2_genbank_its2 <- read.GenBank(Boraginales_its2$its2)
write.dna(Boraginales_its2_genbank_its2, file = "Boraginales_its2.fasta", format = "fasta", append = FALSE)
Boraginales_its2_seqinr <- read.fasta(file = "Boraginales_its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Boraginales_its2_seqinr, names = Boraginales_its2$speciesname, file.out = "Boraginales_its2_sequences.fasta")
setwd(dir ="~/Desktop/mrbayes/Buxales")
Buxales_its1 <- read.csv("Buxales_its1.csv")
Buxales_its1_genbank_its1 <- read.GenBank(Buxales_its1$its1)
write.dna(Buxales_its1_genbank_its1, file = "Buxales_its1.fasta", format = "fasta", append = FALSE)
Buxales_its1_seqinr <- read.fasta(file = "Buxales_its1.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Buxales_its1_seqinr, names = Buxales_its1$speciesname, file.out = "Buxales_its1_sequences.fasta")
Buxales_its2 <- read.csv("Buxales_its2.csv")
Buxales_its2_genbank_its2 <- read.GenBank(Buxales_its2$its2)
write.dna(Buxales_its2_genbank_its2, file = "Buxales_its2.fasta", format = "fasta", append = FALSE)
Buxales_its2_seqinr <- read.fasta(file = "Buxales_its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Buxales_its2_seqinr, names = Buxales_its2$speciesname, file.out = "Buxales_its2_sequences.fasta")
setwd(dir ="~/Desktop/mrbayes/Caryophyllales")
Caryophyllales_its1 <- read.csv("Caryophyllales_its1.csv")
Caryophyllales_its1_genbank_its1 <- read.GenBank(Caryophyllales_its1$its1)
write.dna(Caryophyllales_its1_genbank_its1, file = "Caryophyllales_its1.fasta", format = "fasta", append = FALSE)
Caryophyllales_its1_seqinr <- read.fasta(file = "Caryophyllales_its1.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Caryophyllales_its1_seqinr, names = Caryophyllales_its1$speciesname, file.out = "Caryophyllales_its1_sequences.fasta")
Caryophyllales_its2 <- read.csv("Caryophyllales_its2.csv")
Caryophyllales_its2_genbank_its2 <- read.GenBank(Caryophyllales_its2$its2)
write.dna(Caryophyllales_its2_genbank_its2, file = "Caryophyllales_its2.fasta", format = "fasta", append = FALSE)
Caryophyllales_its2_seqinr <- read.fasta(file = "Caryophyllales_its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Caryophyllales_its2_seqinr, names = Caryophyllales_its2$speciesname, file.out = "Caryophyllales_its2_sequences.fasta")
setwd(dir ="~/Desktop/mrbayes/Celastrales")
Celastrales_its1 <- read.csv("Celastrales_its1.csv")
Celastrales_its1_genbank_its1 <- read.GenBank(Celastrales_its1$its1)
write.dna(Celastrales_its1_genbank_its1, file = "Celastrales_its1.fasta", format = "fasta", append = FALSE)
Celastrales_its2 <- read.csv("Celastrales_its2.csv")
Celastrales_its2_genbank_its2 <- read.GenBank(Celastrales_its2$its2)
write.dna(Celastrales_its2_genbank_its2, file = "Celastrales_its2.fasta", format = "fasta", append = FALSE)
Celastrales_its2_seqinr <- read.fasta(file = "Celastrales_its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Celastrales_its2_seqinr, names = Celastrales_its2$speciesname, file.out = "Celastrales_its2_sequences.fasta")
setwd(dir ="~/Desktop/mrbayes/Cornales")
Cornales_its1 <- read.csv("Cornales_its1.csv")
Cornales_its2 <- read.csv("Cornales_its2.csv")
Cornales_its2_genbank_its2 <- read.GenBank(Cornales_its2$its2)
write.dna(Cornales_its2_genbank_its2, file = "Cornales_its2.fasta", format = "fasta", append = FALSE)
Cornales_its2_seqinr <- read.fasta(file = "Cornales_its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Cornales_its2_seqinr, names = Cornales_its2$speciesname, file.out = "Cornales_its2_sequences.fasta")
setwd(dir ="~/Desktop/mrbayes/Cucurbitales")
Cucurbitales_its2 <- read.csv("Cucurbitales_its2.csv")
Cucurbitales_its2_genbank_its2 <- read.GenBank(Cucurbitales_its2$its2)
write.dna(Cucurbitales_its2_genbank_its2, file = "Cucurbitales_its2.fasta", format = "fasta", append = FALSE)
Cucurbitales_its2_seqinr <- read.fasta(file = "Cucurbitales_its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Cucurbitales_its2_seqinr, names = Cucurbitales_its2$speciesname, file.out = "Cucurbitales_its2_sequences.fasta")
setwd(dir ="~/Desktop/mrbayes/Dilleniales")
Dilleniales_its1 <- read.csv("Dilleniales_its1.csv")
Dilleniales_its2 <- read.csv("Dilleniales_its2.csv")
Dilleniales_its2_genbank_its2 <- read.GenBank(Dilleniales_its2$its2)
write.dna(Dilleniales_its2_genbank_its2, file = "Dilleniales_its2.fasta", format = "fasta", append = FALSE)
Dilleniales_its2_seqinr <- read.fasta(file = "Dilleniales_its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Dilleniales_its2_seqinr, names = Dilleniales_its2$speciesname, file.out = "Dilleniales_its2_sequences.fasta")
setwd(dir ="~/Desktop/mrbayes/Dipsacales")
Dipsacales_its1 <- read.csv("Dipsacales_its1.csv")
Dipsacales_its2 <- read.csv("Dipsacales_its2.csv")
Dipsacales_its2_genbank_its2 <- read.GenBank(Dipsacales_its2$its2)
write.dna(Dipsacales_its2_genbank_its2, file = "Dipsacales_its2.fasta", format = "fasta", append = FALSE)
Dipsacales_its2_seqinr <- read.fasta(file = "Dipsacales_its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Dipsacales_its2_seqinr, names = Dipsacales_its2$speciesname, file.out = "Dipsacales_its2_sequences.fasta")
Dipsacales_its2 <- read.csv("Dipsacales_its2.csv")
Dipsacales_its2_genbank_its2 <- read.GenBank(Dipsacales_its2$its2)
write.dna(Dipsacales_its2_genbank_its2, file = "Dipsacales_its2.fasta", format = "fasta", append = FALSE)
Dipsacales_its2_seqinr <- read.fasta(file = "Dipsacales_its2.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Dipsacales_its2_seqinr, names = Dipsacales_its2$speciesname, file.out = "Dipsacales_its2_sequences.fasta")
