species_list_final <- read.csv("~/Desktop/species_list_final.csv")
previous <- read.csv("~/Desktop/7k_species_file.csv")
joined <- left_join(species_list_final, previous, by = "species_names")
joined <- left_join(species_list_final, previous, by = "speciesnames")
View(species_list_final)
species_list_final <- read.csv("~/Desktop/species_list_final.csv")
previous <- read.csv("~/Desktop/7k_species_file.csv")
joined <- left_join(species_list_final, previous, by = "speciesnames")
View(species_list_final)
View(joined)
write.csv(joined, "~/Desktp/combined_species_list_final")
write.csv(joined, "~/Desktp/combined_species_list_final.csv")
View(joined)
write.csv(joined, "~/Desktop/combined_species_list_final.csv")
species_list_final <- read.csv("~/Desktop/species_list_final.csv")
previous <- read.csv("~/Desktop/7k_species_file.csv")
joined <- left_join(species_list_final, previous, by = "speciesnames")
write.csv(joined, "~/Desktop/combined_species_list_final.csv")
View(joined)
previous <- read.csv("~/Desktop/7k_species_file.csv")
joined <- left_join(species_list_final, previous, by = "speciesnames")
View(joined)
View(previous)
write.csv(joined, "~/Desktop/combined_species_list_final.csv")
read.csv("~/Desktop/semini_species.csv")
semini_species <- read.csv("~/Desktop/semini_species.csv")
library(ape)
library(BIOMASS)
library(dplyr)
library(tidyr)
library(httr)
createCache()
all_combined <-full_join(joined, semini_species, by= c("speciesnames", "matk", "rbcL", "its1", "its2"))
View(species_list_final)
View(all_combined)
all_combined <-full_join(joined, semini_species, by= c("speciesnames", "matk","trnh_psba", "rbcL", "its1", "its2"))
write.csv(all_combined, "~/Desktop/final_dataset.csv ")
write.csv(all_combined, "~/Desktop/final_dataset.csv")
View(corrected)
View(joined)
View(semini_species)
library(ape)
library(BIOMASS)
createCache()
library(taxize)
createCache()
new_temp2 <- correctedTaxo(genus = temp$genus, species = temp$species, useCache = TRUE)
library(BIOMASS)
library(ape)
library(dplyr)
library(tidyr)
library(httr)
help(BIOMASS)
library(BIOMASS)
new_temp2 <- correctedTaxo(genus = temp$genus, species = temp$species, useCache = TRUE)
new_temp2 <- correctTaxo(genus = temp$genus, species = temp$species, useCache = TRUE)
temp <- read.csv("~/Downloads/final_dataset.csv")
new_temp2 <- correctTaxo(genus = temp$genus, species = temp$species, useCache = TRUE)
library(ape)
library(taxize)
library(BIOMASS)
library(taxonomizr)
library(dplyr)
temp <- read.csv("~/Downloads/final_dataset.csv")
new_temp2 <- correctTaxo(genus = temp$genus, species = temp$species, useCache = TRUE)
View(new_temp2)
View(temp)
rm(new_temp2)
rm(new_temp)
#getting the taxonomy of the genus from BIOMASS - getTaxonomy
new_temp <- getTaxonomy(genus = temp$genus, findOrder = TRUE)
library(BIOMASS)
#getting the taxonomy of the genus from BIOMASS - getTaxonomy
new_temp <- getTaxonomy(genus = temp$genus, findOrder = TRUE)
library(ape)
library(ape)
library(taxize)
library(BIOMASS)
#getting the taxonomy of the genus from BIOMASS - getTaxonomy
new_temp <- getTaxonomy(genus = temp$genus, findOrder = TRUE)
View(new_temp)
temp$X <- new_temp$family
View(temp)
temp <- mutate(temp, "order")
library(dplyr)
temp <- mutate(temp, "order")
temp$order <- new_temp$order
temp <- read.csv("~/Downloads/final_dataset.csv")
new_temp[1] <- "genus"
#getting the taxonomy of the genus from BIOMASS - getTaxonomy
new_temp <- getTaxonomy(genus = temp$genus, findOrder = TRUE)
colnames(new_temp) <- c("genus", "family", "order")
temp <- left_join(temp, new_temp, by = "genus")
write.csv(new_temp, "~/Desktop/file_for_grdip.csv")
write.csv(temp, "~/Desktop/file_for_grdip.csv")
### How will I know which one is the accepted name in the taxonomy using this?
library(taxize)
# Example dataframe containing plant names
df <- data.frame(plant_name = c("Acer rubrum", "Abies concolor", "Quercus alba", "Pinus ponderosa"))
# Apply get_accepted_names() to the plant_name column
df$accepted_name <- sapply(df$plant_name, get_accepted_names)
# View the updated dataframe
df
### How will I know which one is the accepted name in the taxonomy using this?
library(taxize)
# Example dataframe containing plant names
df <- data.frame(plant_name = c("Acer rubrum", "Abies concolor", "Quercus alba", "Pinus ponderosa"))
# Apply get_accepted_names() to the plant_name column
df$accepted_name <- sapply(df$plant_name, get_accepted_names)
# View the updated dataframe
df
### How will I know which one is the accepted name in the taxonomy using this?
library(taxize)
# Apply get_accepted_names() to the plant_name column
df$accepted_name <- sapply(df$plant_name, get_accepted_names)
library(ape)
library(dplyr)
library(BIOMASS)
# Apply get_accepted_names() to the plant_name column
df$accepted_name <- sapply(df$plant_name, get_accepted_names)
library(poweR)
# Example list of plant species
species_list <- c("Acer rubrum", "Abies concolor", "Quercus alba", "Pinus ponderosa")
# Initialize the POWO client
pwo_client <- powo_client()
library(poweR)
### Can I get the accepted names of the plant species from a database named "powo" using any R package ?
install.packages("poweR")
library(poweR)
### Can I get the accepted names of the plant species from a database named "powo" using any R package ?
install.packages("powo")
#U.Taxonstand
install.packages("U.Taxonstand")
install.packages("powo")
install.packages("poweR")
install.packages("devtools")
devtools::install_github("barnabywalker/kewr")
download_wcvp()
load_tol()
devtools::install_github("barnabywalker/kewr")
force = TRUE
devtools::install_github("barnabywalker/kewr")
devtools::install_github("barnabywalker/kewr", force = TRUE)
rm(force)
download_wcvp()
lookup_powo("320035-2")
lookup_ipni("987-2", type="publication")
library(poweR)
### Can I get the accepted names of the plant species from a database named "powo" using any R package ?
install.packages("poweR")
library(taxizedb)
june <- read.csv('june.csv', header = TRUE)
t <- tax_name(query = c(june$speciesnames), get = c("phylum","class", "order", "family", "genus"), db = "ncbi", use_entrez())
## Can I also resolve the same for mis-spellings or typos?
# Yes, you can use the correct_names() function from the taxize package to correct misspelled or typo-ridden plant names before using the get_accepted_names() function to obtain the accepted names.
library(taxize)
t <- tax_name(query = c(june$speciesnames), get = c("phylum","class", "order", "family", "genus"), db = "ncbi", use_entrez())
t <- tax_name(query = c(june$speciesnames), get = c("phylum","class", "order", "family", "genus"), db = "ipni", use_entrez())
t <- tax_name(query = c(june$speciesnames), get = c("order", "family", "genus"), db = "ipni")
t <- tax_name(query = c(june$speciesnames), get = c("order", "family", "genus"), db = "ipni")
library(BIOMASS)
june <- read.csv("~/Desktop/jun", header = TRUE)
june <- read.csv("~/Desktop/jun.csv", header = TRUE)
june <- read.csv("~/Desktop/jun.xlsx", header = TRUE)
june <- read.csv("~/Desktop/jun.csv", header = TRUE)
View(june)
june_taxanomy_dataset <- getTaxonomy(june$genus, findOrder =  TRUE)
View(june_taxanomy_dataset)
june_taxanomy_dataset <- getTaxonomy(june$genus)
View(june_taxanomy_dataset)
ndOrder =  TRUE
View(june_taxanomy_dataset)
june_taxanomy_dataset <- getTaxonomy(june$genus)
View(june_taxanomy_dataset)
june_taxanomy_dataset <- getTaxonomy(june$genus, findOrder = TRUE)
View(june_taxanomy_dataset)
write.csv(june_taxanomy_dataset, "~/Desktop/june_taxa.csv")
#install.packages("seqinr")
#install.packages("ape")
# install.packages("tidyverse")
# install.packages("readxl")
library(seqinr)
library(ape)
# library(dplyr)
library(tidyverse)
library(xlsx)
library(ape)x
library(ape)
library(BIOMASS)
library(dplyr)
library(tidyr)
library(httr)
createCache()
library(readr)
rbcL_sequences_final_matk_sequences_10_alignment_2 <- read_csv("Desktop/rbcL_sequences_final - matk_sequences_10 alignment 2.csv")
View(rbcL_sequences_final_matk_sequences_10_alignment_2)
library(readr)
rbcL_matK_names <- read_csv("Desktop/rbcL_sequences_final - matk_sequences_10 alignment 2.csv")
View(rbcL_matK_names)
rm(rbcL_sequences_final_matk_sequences_10_alignment_2)
taxonomy_1 <- getTaxonomy(genus = rbcL_matK_names$genus, findOrder = TRUE)
View(taxonomy_1)
write.csv(taxonomy_1, "~/Desktop/rbcL_matk_constraints", header = TRUE)
write.csv(taxonomy_1, "~/Desktop/rbcL_matk_constraints")
write.csv(taxonomy_1, "~/Desktop/rbcL_matk_constraints.csv")
install.packages("V.PhyloMaker")
install.packages("V.PhyloMaker2")
aln_file <- read.alignment(file = system.file("~/Downloads/Fagales_3502.aln.gz", package = "seqinr"), format= 'clustal')
library(seqinr)
aln_file <- read.alignment(file = system.file("~/Downloads/Fagales_3502.aln.gz", package = "seqinr"), format= 'clustal')
aln_file <- read.alignment(file = system.file("~/Downloads/Fagales_3502.aln.gz", package = "seqinr"), format= 'fasta')
setwd(dir ="~/Desktop/Order-Wise trees/Malpighiales")
library(seqinr)
library(ape)
setwd(dir ="~/Desktop/Order-Wise trees/Malpighiales")
Malpighiales_rbcL <- read.csv("Malpighiales_rbcL.csv")
Malpighiales_rbcL_genbank_rbcL <- read.GenBank(Malpighiales_rbcL$rbcL)
write.dna(Malpighiales_rbcL_genbank_rbcL, file = "Malpighiales_rbcL.fasta", format = "fasta", append = FALSE)
Malpighiales_rbcL_seqinr <- read.fasta(file = "Malpighiales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malpighiales_rbcL_seqinr, names = Malpighiales_rbcL$speciesname, file.out = "Malpighiales_rbcL_sequences.fasta")
Malpighiales_matK <- read.csv("Malpighiales_matK.csv")
Malpighiales_matK_genbank_matK <- read.GenBank(Malpighiales_matK$matk)
write.dna(Malpighiales_matK_genbank_matK, file = "Malpighiales_matK.fasta", format = "fasta", append = FALSE)
Malpighiales_matK_seqinr <- read.fasta(file = "Malpighiales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malpighiales_matK_seqinr, names = Malpighiales_matK$speciesname, file.out = "Malpighiales_matK_sequences.fasta")
Malpighiales_trnH <- read.csv("Malpighiales_trnH.csv")
Malpighiales_trnH_genbank_trnH <- read.GenBank(Malpighiales_trnH$trnh_psba)
write.dna(Malpighiales_trnH_genbank_trnH, file = "Malpighiales_trnH.fasta", format = "fasta", append = FALSE)
Malpighiales_trnH_seqinr <- read.fasta(file = "Malpighiales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malpighiales_trnH_seqinr, names = Malpighiales_trnH$speciesname, file.out = "Malpighiales_trnH_sequences.fasta")
Malpighiales_rbcL <- read.csv("Malpighiales_rbcL.csv")
Malpighiales_rbcL_genbank_rbcL <- read.GenBank(Malpighiales_rbcL$rbcL)
write.dna(Malpighiales_rbcL_genbank_rbcL, file = "Malpighiales_rbcL.fasta", format = "fasta", append = FALSE)
Malpighiales_rbcL_seqinr <- read.fasta(file = "Malpighiales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malpighiales_rbcL_seqinr, names = Malpighiales_rbcL$speciesname, file.out = "Malpighiales_rbcL_sequences.fasta")
Malpighiales_matK <- read.csv("Malpighiales_matK.csv")
Malpighiales_matK_genbank_matK <- read.GenBank(Malpighiales_matK$matk)
write.dna(Malpighiales_matK_genbank_matK, file = "Malpighiales_matK.fasta", format = "fasta", append = FALSE)
Malpighiales_matK_seqinr <- read.fasta(file = "Malpighiales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malpighiales_matK_seqinr, names = Malpighiales_matK$speciesname, file.out = "Malpighiales_matK_sequences.fasta")
Malpighiales_trnH <- read.csv("Malpighiales_trnH.csv")
Malpighiales_trnH_genbank_trnH <- read.GenBank(Malpighiales_trnH$trnh_psba)
write.dna(Malpighiales_trnH_genbank_trnH, file = "Malpighiales_trnH.fasta", format = "fasta", append = FALSE)
Malpighiales_trnH_seqinr <- read.fasta(file = "Malpighiales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malpighiales_trnH_seqinr, names = Malpighiales_trnH$speciesname, file.out = "Malpighiales_trnH_sequences.fasta")
Malpighiales_trnH <- read.csv("Malpighiales_trnH.csv")
Malpighiales_trnH_genbank_trnH <- read.GenBank(Malpighiales_trnH$trnh_psba)
write.dna(Malpighiales_trnH_genbank_trnH, file = "Malpighiales_trnH.fasta", format = "fasta", append = FALSE)
Malpighiales_trnH_seqinr <- read.fasta(file = "Malpighiales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malpighiales_trnH_seqinr, names = Malpighiales_trnH$speciesname, file.out = "Malpighiales_trnH_sequences.fasta")
Malpighiales_trnH <- read.csv("Malpighiales_trnH.csv")
View(Malpighiales_trnH)
Malpighiales_trnH_genbank_trnH <- read.GenBank(Malpighiales_trnH$trnh_psba)
Malpighiales_trnH <- read.csv("Malpighiales_trnH.csv")
Malpighiales_trnH_genbank_trnH <- read.GenBank(Malpighiales_trnH$trnh_psba)
write.dna(Malpighiales_trnH_genbank_trnH, file = "Malpighiales_trnH.fasta", format = "fasta", append = FALSE)
Malpighiales_trnH_seqinr <- read.fasta(file = "Malpighiales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malpighiales_trnH_seqinr, names = Malpighiales_trnH$speciesname, file.out = "Malpighiales_trnH_sequences.fasta")
setwd(dir ="~/Desktop/Order-Wise trees/Malvales")
Malvales_rbcL <- read.csv("Malvales_rbcL.csv")
Malvales_rbcL_genbank_rbcL <- read.GenBank(Malvales_rbcL$rbcL)
write.dna(Malvales_rbcL_genbank_rbcL, file = "Malvales_rbcL.fasta", format = "fasta", append = FALSE)
Malvales_rbcL_seqinr <- read.fasta(file = "Malvales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malvales_rbcL_seqinr, names = Malvales_rbcL$speciesname, file.out = "Malvales_rbcL_sequences.fasta")
Malvales_matK <- read.csv("Malvales_matK.csv")
Malvales_matK_genbank_matK <- read.GenBank(Malvales_matK$matk)
write.dna(Malvales_matK_genbank_matK, file = "Malvales_matK.fasta", format = "fasta", append = FALSE)
Malvales_matK_seqinr <- read.fasta(file = "Malvales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malvales_matK_seqinr, names = Malvales_matK$speciesname, file.out = "Malvales_matK_sequences.fasta")
Malvales_trnH <- read.csv("Malvales_trnH.csv")
setwd(dir ="~/Desktop/Order-Wise trees/Malvales")
Malvales_rbcL <- read.csv("Malvales_rbcL.csv")
Malvales_rbcL <- read.csv("Malvales_rbcL.csv")
Malvales_rbcL_genbank_rbcL <- read.GenBank(Malvales_rbcL$rbcL)
write.dna(Malvales_rbcL_genbank_rbcL, file = "Malvales_rbcL.fasta", format = "fasta", append = FALSE)
Malvales_rbcL <- read.csv("Malvales_rbcL.csv")
Malvales_rbcL_genbank_rbcL <- read.GenBank(Malvales_rbcL$rbcL)
write.dna(Malvales_rbcL_genbank_rbcL, file = "Malvales_rbcL.fasta", format = "fasta", append = FALSE)
Malvales_rbcL_seqinr <- read.fasta(file = "Malvales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malvales_rbcL_seqinr, names = Malvales_rbcL$speciesname, file.out = "Malvales_rbcL_sequences.fasta")
Malvales_matK <- read.csv("Malvales_matK.csv")
Malvales_matK_genbank_matK <- read.GenBank(Malvales_matK$matk)
write.dna(Malvales_matK_genbank_matK, file = "Malvales_matK.fasta", format = "fasta", append = FALSE)
Malvales_matK_seqinr <- read.fasta(file = "Malvales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malvales_matK_seqinr, names = Malvales_matK$speciesname, file.out = "Malvales_matK_sequences.fasta")
Malvales_trnH <- read.csv("Malvales_trnH.csv")
Malvales_trnH_genbank_trnH <- read.GenBank(Malvales_trnH$trnh_psba)
write.dna(Malvales_trnH_genbank_trnH, file = "Malvales_trnH.fasta", format = "fasta", append = FALSE)
Malvales_trnH_seqinr <- read.fasta(file = "Malvales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malvales_trnH_seqinr, names = Malvales_trnH$speciesname, file.out = "Malvales_trnH_sequences.fasta")
Malvales_rbcL <- read.csv("Malvales_rbcL.csv")
Malvales_rbcL_genbank_rbcL <- read.GenBank(Malvales_rbcL$rbcL)
write.dna(Malvales_rbcL_genbank_rbcL, file = "Malvales_rbcL.fasta", format = "fasta", append = FALSE)
Malvales_rbcL_seqinr <- read.fasta(file = "Malvales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malvales_rbcL_seqinr, names = Malvales_rbcL$speciesname, file.out = "Malvales_rbcL_sequences.fasta")
Malvales_matK <- read.csv("Malvales_matK.csv")
Malvales_matK_genbank_matK <- read.GenBank(Malvales_matK$matk)
write.dna(Malvales_matK_genbank_matK, file = "Malvales_matK.fasta", format = "fasta", append = FALSE)
Malvales_matK_seqinr <- read.fasta(file = "Malvales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malvales_matK_seqinr, names = Malvales_matK$speciesname, file.out = "Malvales_matK_sequences.fasta")
Malvales_trnH <- read.csv("Malvales_trnH.csv")
Malvales_trnH_genbank_trnH <- read.GenBank(Malvales_trnH$trnh_psba)
write.dna(Malvales_trnH_genbank_trnH, file = "Malvales_trnH.fasta", format = "fasta", append = FALSE)
Malvales_trnH_seqinr <- read.fasta(file = "Malvales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malvales_trnH_seqinr, names = Malvales_trnH$speciesname, file.out = "Malvales_trnH_sequences.fasta")
Malvales_trnH <- read.csv("Malvales_trnH.csv")
Malvales_trnH_genbank_trnH <- read.GenBank(Malvales_trnH$trnh_psba)
write.dna(Malvales_trnH_genbank_trnH, file = "Malvales_trnH.fasta", format = "fasta", append = FALSE)
Malvales_trnH_seqinr <- read.fasta(file = "Malvales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malvales_trnH_seqinr, names = Malvales_trnH$speciesname, file.out = "Malvales_trnH_sequences.fasta")
Malvales_trnH <- read.csv("Malvales_trnH.csv")
Malvales_trnH_genbank_trnH <- read.GenBank(Malvales_trnH$trnh_psba)
write.dna(Malvales_trnH_genbank_trnH, file = "Malvales_trnH.fasta", format = "fasta", append = FALSE)
Malvales_trnH_seqinr <- read.fasta(file = "Malvales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malvales_trnH_seqinr, names = Malvales_trnH$speciesname, file.out = "Malvales_trnH_sequences.fasta")
Malvales_trnH <- read.csv("Malvales_trnH.csv")
Malvales_trnH_genbank_trnH <- read.GenBank(Malvales_trnH$trnh_psba)
write.dna(Malvales_trnH_genbank_trnH, file = "Malvales_trnH.fasta", format = "fasta", append = FALSE)
Malvales_trnH_seqinr <- read.fasta(file = "Malvales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malvales_trnH_seqinr, names = Malvales_trnH$speciesname, file.out = "Malvales_trnH_sequences.fasta")
Malvales_trnH <- read.csv("Malvales_trnH.csv")
Malvales_trnH_genbank_trnH <- read.GenBank(Malvales_trnH$trnh_psba)
write.dna(Malvales_trnH_genbank_trnH, file = "Malvales_trnH.fasta", format = "fasta", append = FALSE)
Malvales_trnH_seqinr <- read.fasta(file = "Malvales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malvales_trnH_seqinr, names = Malvales_trnH$speciesname, file.out = "Malvales_trnH_sequences.fasta")
Malvales_trnH <- read.csv("Malvales_trnH.csv")
Malvales_trnH_genbank_trnH <- read.GenBank(Malvales_trnH$trnh_psba)
write.dna(Malvales_trnH_genbank_trnH, file = "Malvales_trnH.fasta", format = "fasta", append = FALSE)
Malvales_trnH_seqinr <- read.fasta(file = "Malvales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malvales_trnH_seqinr, names = Malvales_trnH$speciesname, file.out = "Malvales_trnH_sequences.fasta")
Malvales_trnH <- read.csv("Malvales_trnH.csv")
Malvales_trnH_genbank_trnH <- read.GenBank(Malvales_trnH$trnh_psba)
write.dna(Malvales_trnH_genbank_trnH, file = "Malvales_trnH.fasta", format = "fasta", append = FALSE)
Malvales_trnH_seqinr <- read.fasta(file = "Malvales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Malvales_trnH_seqinr, names = Malvales_trnH$speciesname, file.out = "Malvales_trnH_sequences.fasta")
library(seqinr)
library(ape)
setwd(dir ="~/Desktop/Order-Wise trees/Myrtales")
Myrtales_rbcL <- read.csv("Myrtales_rbcL.csv")
Myrtales_rbcL_genbank_rbcL <- read.GenBank(Myrtales_rbcL$rbcL)
write.dna(Myrtales_rbcL_genbank_rbcL, file = "Myrtales_rbcL.fasta", format = "fasta", append = FALSE)
Myrtales_rbcL <- read.csv("Myrtales_rbcL.csv")
Myrtales_rbcL_genbank_rbcL <- read.GenBank(Myrtales_rbcL$rbcL)
write.dna(Myrtales_rbcL_genbank_rbcL, file = "Myrtales_rbcL.fasta", format = "fasta", append = FALSE)
Myrtales_rbcL_seqinr <- read.fasta(file = "Myrtales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Myrtales_rbcL_seqinr, names = Myrtales_rbcL$speciesname, file.out = "Myrtales_rbcL_sequences.fasta")
Myrtales_matK <- read.csv("Myrtales_matK.csv")
Myrtales_matK_genbank_matK <- read.GenBank(Myrtales_matK$matk)
write.dna(Myrtales_matK_genbank_matK, file = "Myrtales_matK.fasta", format = "fasta", append = FALSE)
Myrtales_matK_seqinr <- read.fasta(file = "Myrtales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Myrtales_matK_seqinr, names = Myrtales_matK$speciesname, file.out = "Myrtales_matK_sequences.fasta")
Myrtales_trnH <- read.csv("Myrtales_trnH.csv")
Myrtales_trnH_genbank_trnH <- read.GenBank(Myrtales_trnH$trnh_psba)
write.dna(Myrtales_trnH_genbank_trnH, file = "Myrtales_trnH.fasta", format = "fasta", append = FALSE)
Myrtales_trnH_seqinr <- read.fasta(file = "Myrtales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Myrtales_trnH_seqinr, names = Myrtales_trnH$speciesname, file.out = "Myrtales_trnH_sequences.fasta")
Myrtales_rbcL <- read.csv("Myrtales_rbcL.csv")
Myrtales_rbcL_genbank_rbcL <- read.GenBank(Myrtales_rbcL$rbcL)
write.dna(Myrtales_rbcL_genbank_rbcL, file = "Myrtales_rbcL.fasta", format = "fasta", append = FALSE)
Myrtales_rbcL_seqinr <- read.fasta(file = "Myrtales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Myrtales_rbcL_seqinr, names = Myrtales_rbcL$speciesname, file.out = "Myrtales_rbcL_sequences.fasta")
Myrtaceae_trnH <- read.csv("Myrtaceae_trnH.csv")
Myrtaceae_trnH_genbank_trnH <- read.GenBank(Myrtaceae_trnH$trnh_psba)
write.dna(Myrtaceae_trnH_genbank_trnH, file = "Myrtaceae_trnH.fasta", format = "fasta", append = FALSE)
Myrtaceae_trnH_seqinr <- read.fasta(file = "Myrtaceae_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Myrtaceae_trnH_seqinr, names = Myrtaceae_trnH$speciesname, file.out = "Myrtaceae_trnH_sequences.fasta")
Lythraceae_trnH <- read.csv("Lythraceae_trnH.csv")
Lythraceae_trnH_genbank_trnH <- read.GenBank(Lythraceae_trnH$trnh_psba)
write.dna(Lythraceae_trnH_genbank_trnH, file = "Lythraceae_trnH.fasta", format = "fasta", append = FALSE)
Lythraceae_trnH_seqinr <- read.fasta(file = "Lythraceae_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Lythraceae_trnH_seqinr, names = Lythraceae_trnH$speciesname, file.out = "Lythraceae_trnH_sequences.fasta")
Combretaceae_trnH <- read.csv("Combretaceae_trnH.csv")
Combretaceae_trnH_genbank_trnH <- read.GenBank(Combretaceae_trnH$trnh_psba)
write.dna(Combretaceae_trnH_genbank_trnH, file = "Combretaceae_trnH.fasta", format = "fasta", append = FALSE)
Combretaceae_trnH_seqinr <- read.fasta(file = "Combretaceae_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Combretaceae_trnH_seqinr, names = Combretaceae_trnH$speciesname, file.out = "Combretaceae_trnH_sequences.fasta")
Myrtales_trnH <- read.csv("Myrtales_trnH.csv")
Myrtales_trnH_genbank_trnH <- read.GenBank(Myrtales_trnH$trnh_psba)
write.dna(Myrtales_trnH_genbank_trnH, file = "Myrtales_trnH.fasta", format = "fasta", append = FALSE)
Myrtales_trnH_seqinr <- read.fasta(file = "Myrtales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Myrtales_trnH_seqinr, names = Myrtales_trnH$speciesname, file.out = "Myrtales_trnH_sequences.fasta")
library(seqinr)
library(ape)
setwd(dir ="~/Desktop/Order-Wise trees/Oxalidales")
Oxalidales_rbcL <- read.csv("Oxalidales_rbcL.csv")
Oxalidales_rbcL_genbank_rbcL <- read.GenBank(Oxalidales_rbcL$rbcL)
write.dna(Oxalidales_rbcL_genbank_rbcL, file = "Oxalidales_rbcL.fasta", format = "fasta", append = FALSE)
Oxalidales_rbcL_seqinr <- read.fasta(file = "Oxalidales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Oxalidales_rbcL_seqinr, names = Oxalidales_rbcL$speciesname, file.out = "Oxalidales_rbcL_sequences.fasta")
Oxalidales_matK <- read.csv("Oxalidales_matK.csv")
Oxalidales_matK_genbank_matK <- read.GenBank(Oxalidales_matK$matk)
write.dna(Oxalidales_matK_genbank_matK, file = "Oxalidales_matK.fasta", format = "fasta", append = FALSE)
Oxalidales_matK_seqinr <- read.fasta(file = "Oxalidales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Oxalidales_matK_seqinr, names = Oxalidales_matK$speciesname, file.out = "Oxalidales_matK_sequences.fasta")
Oxalidales_trnH <- read.csv("Oxalidales_trnH.csv")
Oxalidales_trnH_genbank_trnH <- read.GenBank(Oxalidales_trnH$trnh_psba)
write.dna(Oxalidales_trnH_genbank_trnH, file = "Oxalidales_trnH.fasta", format = "fasta", append = FALSE)
Oxalidales_trnH_seqinr <- read.fasta(file = "Oxalidales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Oxalidales_trnH_seqinr, names = Oxalidales_trnH$speciesname, file.out = "Oxalidales_trnH_sequences.fasta")
setwd(dir ="~/Desktop/Order-Wise trees/Pinales")
Pinales_rbcL <- read.csv("Pinales_rbcL.csv")
Pinales_rbcL_genbank_rbcL <- read.GenBank(Pinales_rbcL$rbcL)
write.dna(Pinales_rbcL_genbank_rbcL, file = "Pinales_rbcL.fasta", format = "fasta", append = FALSE)
Pinales_rbcL_seqinr <- read.fasta(file = "Pinales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Pinales_rbcL_seqinr, names = Pinales_rbcL$speciesname, file.out = "Pinales_rbcL_sequences.fasta")
Pinales_matK <- read.csv("Pinales_matK.csv")
Pinales_matK_genbank_matK <- read.GenBank(Pinales_matK$matk)
write.dna(Pinales_matK_genbank_matK, file = "Pinales_matK.fasta", format = "fasta", append = FALSE)
Pinales_matK_seqinr <- read.fasta(file = "Pinales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Pinales_matK_seqinr, names = Pinales_matK$speciesname, file.out = "Pinales_matK_sequences.fasta")
Pinales_trnH <- read.csv("Pinales_trnH.csv")
Pinales_trnH_genbank_trnH <- read.GenBank(Pinales_trnH$trnh_psba)
write.dna(Pinales_trnH_genbank_trnH, file = "Pinales_trnH.fasta", format = "fasta", append = FALSE)
Pinales_trnH_seqinr <- read.fasta(file = "Pinales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Pinales_trnH_seqinr, names = Pinales_trnH$speciesname, file.out = "Pinales_trnH_sequences.fasta")
Pinales_trnH <- read.csv("Pinales_trnH.csv")
Pinales_trnH_genbank_trnH <- read.GenBank(Pinales_trnH$trnh_psba)
write.dna(Pinales_trnH_genbank_trnH, file = "Pinales_trnH.fasta", format = "fasta", append = FALSE)
Pinales_trnH_seqinr <- read.fasta(file = "Pinales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Pinales_trnH_seqinr, names = Pinales_trnH$speciesname, file.out = "Pinales_trnH_sequences.fasta")
library(seqinr)
library(ape)
setwd(dir ="~/Desktop/Order-Wise trees/Poales")
Poales_rbcL <- read.csv("Poales_rbcL.csv")
Poales_rbcL_genbank_rbcL <- read.GenBank(Poales_rbcL$rbcL)
write.dna(Poales_rbcL_genbank_rbcL, file = "Poales_rbcL.fasta", format = "fasta", append = FALSE)
Poales_rbcL_seqinr <- read.fasta(file = "Poales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Poales_rbcL_seqinr, names = Poales_rbcL$speciesname, file.out = "Poales_rbcL_sequences.fasta")
Poales_matK <- read.csv("Poales_matK.csv")
Poales_matK_genbank_matK <- read.GenBank(Poales_matK$matk)
write.dna(Poales_matK_genbank_matK, file = "Poales_matK.fasta", format = "fasta", append = FALSE)
Poales_matK_seqinr <- read.fasta(file = "Poales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Poales_matK_seqinr, names = Poales_matK$speciesname, file.out = "Poales_matK_sequences.fasta")
Poales_trnH <- read.csv("Poales_trnH.csv")
Poales_trnH_genbank_trnH <- read.GenBank(Poales_trnH$trnh_psba)
write.dna(Poales_trnH_genbank_trnH, file = "Poales_trnH.fasta", format = "fasta", append = FALSE)
Poales_trnH_seqinr <- read.fasta(file = "Poales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Poales_trnH_seqinr, names = Poales_trnH$speciesname, file.out = "Poales_trnH_sequences.fasta")
library(seqinr)
library(ape)
setwd(dir ="~/Desktop/Order-Wise trees/Proteales")
Proteales_rbcL <- read.csv("Proteales_rbcL.csv")
Proteales_rbcL_genbank_rbcL <- read.GenBank(Proteales_rbcL$rbcL)
write.dna(Proteales_rbcL_genbank_rbcL, file = "Proteales_rbcL.fasta", format = "fasta", append = FALSE)
Proteales_rbcL_seqinr <- read.fasta(file = "Proteales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Proteales_rbcL_seqinr, names = Proteales_rbcL$speciesname, file.out = "Proteales_rbcL_sequences.fasta")
Proteales_matK <- read.csv("Proteales_matK.csv")
Proteales_matK_genbank_matK <- read.GenBank(Proteales_matK$matk)
write.dna(Proteales_matK_genbank_matK, file = "Proteales_matK.fasta", format = "fasta", append = FALSE)
Proteales_matK_seqinr <- read.fasta(file = "Proteales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Proteales_matK_seqinr, names = Proteales_matK$speciesname, file.out = "Proteales_matK_sequences.fasta")
Proteales_trnH <- read.csv("Proteales_trnH.csv")
Proteales_trnH_genbank_trnH <- read.GenBank(Proteales_trnH$trnh_psba)
write.dna(Proteales_trnH_genbank_trnH, file = "Proteales_trnH.fasta", format = "fasta", append = FALSE)
Proteales_trnH_seqinr <- read.fasta(file = "Proteales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Proteales_trnH_seqinr, names = Proteales_trnH$speciesname, file.out = "Proteales_trnH_sequences.fasta")
Proteales_trnH <- read.csv("Proteales_trnH.csv")
Proteales_trnH_genbank_trnH <- read.GenBank(Proteales_trnH$trnh_psba)
write.dna(Proteales_trnH_genbank_trnH, file = "Proteales_trnH.fasta", format = "fasta", append = FALSE)
Proteales_trnH_seqinr <- read.fasta(file = "Proteales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Proteales_trnH_seqinr, names = Proteales_trnH$speciesname, file.out = "Proteales_trnH_sequences.fasta")
Proteales_trnH <- read.csv("Proteales_trnH.csv")
Proteales_trnH_genbank_trnH <- read.GenBank(Proteales_trnH$trnh_psba)
write.dna(Proteales_trnH_genbank_trnH, file = "Proteales_trnH.fasta", format = "fasta", append = FALSE)
Proteales_trnH_seqinr <- read.fasta(file = "Proteales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Proteales_trnH_seqinr, names = Proteales_trnH$speciesname, file.out = "Proteales_trnH_sequences.fasta")
setwd(dir ="~/Desktop/Order-Wise trees/Rosales")
Rosales_rbcL <- read.csv("Rosales_rbcL.csv")
Rosales_rbcL_genbank_rbcL <- read.GenBank(Rosales_rbcL$rbcL)
write.dna(Rosales_rbcL_genbank_rbcL, file = "Rosales_rbcL.fasta", format = "fasta", append = FALSE)
Rosales_rbcL_seqinr <- read.fasta(file = "Rosales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Rosales_rbcL_seqinr, names = Rosales_rbcL$speciesname, file.out = "Rosales_rbcL_sequences.fasta")
Rosales_matK <- read.csv("Rosales_matK.csv")
Rosales_matK_genbank_matK <- read.GenBank(Rosales_matK$matk)
write.dna(Rosales_matK_genbank_matK, file = "Rosales_matK.fasta", format = "fasta", append = FALSE)
Rosales_matK_seqinr <- read.fasta(file = "Rosales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Rosales_matK_seqinr, names = Rosales_matK$speciesname, file.out = "Rosales_matK_sequences.fasta")
Rosales_trnH <- read.csv("Rosales_trnH.csv")
Rosales_trnH_genbank_trnH <- read.GenBank(Rosales_trnH$trnh_psba)
write.dna(Rosales_trnH_genbank_trnH, file = "Rosales_trnH.fasta", format = "fasta", append = FALSE)
Rosales_trnH_seqinr <- read.fasta(file = "Rosales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Rosales_trnH_seqinr, names = Rosales_trnH$speciesname, file.out = "Rosales_trnH_sequences.fasta")
Rosales_rbcL <- read.csv("Rosales_rbcL.csv")
Rosales_rbcL_genbank_rbcL <- read.GenBank(Rosales_rbcL$rbcL)
write.dna(Rosales_rbcL_genbank_rbcL, file = "Rosales_rbcL.fasta", format = "fasta", append = FALSE)
Rosales_rbcL_seqinr <- read.fasta(file = "Rosales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Rosales_rbcL_seqinr, names = Rosales_rbcL$speciesname, file.out = "Rosales_rbcL_sequences.fasta")
Rosales_trnH <- read.csv("Rosales_trnH.csv")
Rosales_trnH_genbank_trnH <- read.GenBank(Rosales_trnH$trnh_psba)
write.dna(Rosales_trnH_genbank_trnH, file = "Rosales_trnH.fasta", format = "fasta", append = FALSE)
Rosales_trnH_seqinr <- read.fasta(file = "Rosales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Rosales_trnH_seqinr, names = Rosales_trnH$speciesname, file.out = "Rosales_trnH_sequences.fasta")
Rosales_trnH <- read.csv("Rosales_trnH.csv")
Rosales_trnH_genbank_trnH <- read.GenBank(Rosales_trnH$trnh_psba)
write.dna(Rosales_trnH_genbank_trnH, file = "Rosales_trnH.fasta", format = "fasta", append = FALSE)
Rosales_trnH_seqinr <- read.fasta(file = "Rosales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Rosales_trnH_seqinr, names = Rosales_trnH$speciesname, file.out = "Rosales_trnH_sequences.fasta")
Rosales_trnH <- read.csv("Rosales_trnH.csv")
Rosales_trnH_genbank_trnH <- read.GenBank(Rosales_trnH$trnh_psba)
write.dna(Rosales_trnH_genbank_trnH, file = "Rosales_trnH.fasta", format = "fasta", append = FALSE)
Rosales_trnH_seqinr <- read.fasta(file = "Rosales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Rosales_trnH_seqinr, names = Rosales_trnH$speciesname, file.out = "Rosales_trnH_sequences.fasta")
Rosales_trnH <- read.csv("Rosales_trnH.csv")
Rosales_trnH_genbank_trnH <- read.GenBank(Rosales_trnH$trnh_psba)
write.dna(Rosales_trnH_genbank_trnH, file = "Rosales_trnH.fasta", format = "fasta", append = FALSE)
Rosales_trnH_seqinr <- read.fasta(file = "Rosales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Rosales_trnH_seqinr, names = Rosales_trnH$speciesname, file.out = "Rosales_trnH_sequences.fasta")
Rosales_trnH <- read.csv("Rosales_trnH.csv")
Rosales_trnH_genbank_trnH <- read.GenBank(Rosales_trnH$trnh_psba)
write.dna(Rosales_trnH_genbank_trnH, file = "Rosales_trnH.fasta", format = "fasta", append = FALSE)
Rosales_trnH_seqinr <- read.fasta(file = "Rosales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Rosales_trnH_seqinr, names = Rosales_trnH$speciesname, file.out = "Rosales_trnH_sequences.fasta")
