View(species_list_final)
joined <- left_join(species_list_final, previous, by = "species_names")
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')
library(seqinr)
library(ape)
setwd(dir ="~/Desktop/Order-Wise trees/Caryophyllales")
Caryophyllales_trnH <- read.csv("Caryophyllales_trnH.csv")
Caryophyllales_trnH_genbank_trnH <- read.GenBank(Caryophyllales_trnH$trnh_psba)
write.dna(Caryophyllales_trnH_genbank_trnH, file = "Caryophyllales_trnH.fasta", format = "fasta", append = FALSE)
Caryophyllales_trnH_seqinr <- read.fasta(file = "Caryophyllales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Caryophyllales_trnH_seqinr, names = Caryophyllales_trnH$speciesname, file.out = "Caryophyllales_trnH_sequences.fasta")
setwd(dir ="~/Desktop/Order-Wise trees/Celastrales")
Celastrales_rbcL <- read.csv("Celastrales_rbcL.csv")
Celastrales_rbcL_genbank_rbcL <- read.GenBank(Celastrales_rbcL$rbcL)
write.dna(Celastrales_rbcL_genbank_rbcL, file = "Celastrales_rbcL.fasta", format = "fasta", append = FALSE)
Celastrales_rbcL_seqinr <- read.fasta(file = "Celastrales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Celastrales_rbcL_seqinr, names = Celastrales_rbcL$speciesname, file.out = "Celastrales_rbcL_sequences.fasta")
Celastrales_matK <- read.csv("Celastrales_matK.csv")
Celastrales_matK_genbank_matK <- read.GenBank(Celastrales_matK$matk)
write.dna(Celastrales_matK_genbank_matK, file = "Celastrales_matK.fasta", format = "fasta", append = FALSE)
Celastrales_matK_seqinr <- read.fasta(file = "Celastrales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Celastrales_matK_seqinr, names = Celastrales_matK$speciesname, file.out = "Celastrales_matK_sequences.fasta")
Celastrales_trnH <- read.csv("Celastrales_trnH.csv")
Celastrales_trnH_genbank_trnH <- read.GenBank(Celastrales_trnH$trnh_psba)
write.dna(Celastrales_trnH_genbank_trnH, file = "Celastrales_trnH.fasta", format = "fasta", append = FALSE)
Celastrales_trnH_seqinr <- read.fasta(file = "Celastrales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Celastrales_trnH_seqinr, names = Celastrales_trnH$speciesname, file.out = "Celastrales_trnH_sequences.fasta")
setwd(dir ="~/Desktop/Order-Wise trees/Cornales")
Cornales_rbcL <- read.csv("Cornales_rbcL.csv")
Cornales_rbcL_genbank_rbcL <- read.GenBank(Cornales_rbcL$rbcL)
write.dna(Cornales_rbcL_genbank_rbcL, file = "Cornales_rbcL.fasta", format = "fasta", append = FALSE)
Cornales_rbcL_seqinr <- read.fasta(file = "Cornales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Cornales_rbcL_seqinr, names = Cornales_rbcL$speciesname, file.out = "Cornales_rbcL_sequences.fasta")
Cornales_matK <- read.csv("Cornales_matK.csv")
Cornales_matK_genbank_matK <- read.GenBank(Cornales_matK$matk)
write.dna(Cornales_matK_genbank_matK, file = "Cornales_matK.fasta", format = "fasta", append = FALSE)
Cornales_matK_seqinr <- read.fasta(file = "Cornales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Cornales_matK_seqinr, names = Cornales_matK$speciesname, file.out = "Cornales_matK_sequences.fasta")
Cornales_trnH <- read.csv("Cornales_trnH.csv")
Cornales_trnH_genbank_trnH <- read.GenBank(Cornales_trnH$trnh_psba)
write.dna(Cornales_trnH_genbank_trnH, file = "Cornales_trnH.fasta", format = "fasta", append = FALSE)
Cornales_trnH_seqinr <- read.fasta(file = "Cornales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Cornales_trnH_seqinr, names = Cornales_trnH$speciesname, file.out = "Cornales_trnH_sequences.fasta")
setwd(dir ="~/Desktop/Order-Wise trees/Cycadales")
Cycadales_rbcL <- read.csv("Cycadales_rbcL.csv")
Cycadales_rbcL_genbank_rbcL <- read.GenBank(Cycadales_rbcL$rbcL)
write.dna(Cycadales_rbcL_genbank_rbcL, file = "Cycadales_rbcL.fasta", format = "fasta", append = FALSE)
Cycadales_rbcL_seqinr <- read.fasta(file = "Cycadales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Cycadales_rbcL_seqinr, names = Cycadales_rbcL$speciesname, file.out = "Cycadales_rbcL_sequences.fasta")
Cycadales_matK <- read.csv("Cycadales_matK.csv")
Cycadales_matK_genbank_matK <- read.GenBank(Cycadales_matK$matk)
write.dna(Cycadales_matK_genbank_matK, file = "Cycadales_matK.fasta", format = "fasta", append = FALSE)
Cycadales_matK_seqinr <- read.fasta(file = "Cycadales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Cycadales_matK_seqinr, names = Cycadales_matK$speciesname, file.out = "Cycadales_matK_sequences.fasta")
Cycadales_trnH <- read.csv("Cycadales_trnH.csv")
Cycadales_trnH_genbank_trnH <- read.GenBank(Cycadales_trnH$trnh_psba)
write.dna(Cycadales_trnH_genbank_trnH, file = "Cycadales_trnH.fasta", format = "fasta", append = FALSE)
Cycadales_trnH_seqinr <- read.fasta(file = "Cycadales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Cycadales_trnH_seqinr, names = Cycadales_trnH$speciesname, file.out = "Cycadales_trnH_sequences.fasta")
setwd(dir ="~/Desktop/Order-Wise trees/Dilleniales")
Dilleniales_rbcL <- read.csv("Dilleniales_rbcL.csv")
Dilleniales_rbcL_genbank_rbcL <- read.GenBank(Dilleniales_rbcL$rbcL)
write.dna(Dilleniales_rbcL_genbank_rbcL, file = "Dilleniales_rbcL.fasta", format = "fasta", append = FALSE)
Dilleniales_rbcL_seqinr <- read.fasta(file = "Dilleniales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Dilleniales_rbcL_seqinr, names = Dilleniales_rbcL$speciesname, file.out = "Dilleniales_rbcL_sequences.fasta")
Dilleniales_matK <- read.csv("Dilleniales_matK.csv")
Dilleniales_matK_genbank_matK <- read.GenBank(Dilleniales_matK$matk)
write.dna(Dilleniales_matK_genbank_matK, file = "Dilleniales_matK.fasta", format = "fasta", append = FALSE)
Dilleniales_matK_seqinr <- read.fasta(file = "Dilleniales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Dilleniales_matK_seqinr, names = Dilleniales_matK$speciesname, file.out = "Dilleniales_matK_sequences.fasta")
Dilleniales_trnH <- read.csv("Dilleniales_trnH.csv")
Dilleniales_trnH_genbank_trnH <- read.GenBank(Dilleniales_trnH$trnh_psba)
write.dna(Dilleniales_trnH_genbank_trnH, file = "Dilleniales_trnH.fasta", format = "fasta", append = FALSE)
Dilleniales_trnH_seqinr <- read.fasta(file = "Dilleniales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Dilleniales_trnH_seqinr, names = Dilleniales_trnH$speciesname, file.out = "Dilleniales_trnH_sequences.fasta")
setwd(dir ="~/Desktop/Order-Wise trees/Dipsacales")
Dipsacales_rbcL <- read.csv("Dipsacales_rbcL.csv")
Dipsacales_rbcL_genbank_rbcL <- read.GenBank(Dipsacales_rbcL$rbcL)
write.dna(Dipsacales_rbcL_genbank_rbcL, file = "Dipsacales_rbcL.fasta", format = "fasta", append = FALSE)
Dipsacales_rbcL_seqinr <- read.fasta(file = "Dipsacales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Dipsacales_rbcL_seqinr, names = Dipsacales_rbcL$speciesname, file.out = "Dipsacales_rbcL_sequences.fasta")
Dipsacales_matK <- read.csv("Dipsacales_matK.csv")
Dipsacales_matK_genbank_matK <- read.GenBank(Dipsacales_matK$matk)
write.dna(Dipsacales_matK_genbank_matK, file = "Dipsacales_matK.fasta", format = "fasta", append = FALSE)
Dipsacales_matK_seqinr <- read.fasta(file = "Dipsacales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Dipsacales_matK_seqinr, names = Dipsacales_matK$speciesname, file.out = "Dipsacales_matK_sequences.fasta")
Dipsacales_trnH <- read.csv("Dipsacales_trnH.csv")
Dipsacales_trnH_genbank_trnH <- read.GenBank(Dipsacales_trnH$trnh_psba)
write.dna(Dipsacales_trnH_genbank_trnH, file = "Dipsacales_trnH.fasta", format = "fasta", append = FALSE)
Dipsacales_trnH_seqinr <- read.fasta(file = "Dipsacales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Dipsacales_trnH_seqinr, names = Dipsacales_trnH$speciesname, file.out = "Dipsacales_trnH_sequences.fasta")
setwd(dir ="~/Desktop/Order-Wise trees/Fabales")
Fabales_rbcL <- read.csv("Fabales_rbcL.csv")
Fabales_rbcL_genbank_rbcL <- read.GenBank(Fabales_rbcL$rbcL)
write.dna(Fabales_rbcL_genbank_rbcL, file = "Fabales_rbcL.fasta", format = "fasta", append = FALSE)
Fabales_rbcL_seqinr <- read.fasta(file = "Fabales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Fabales_rbcL_seqinr, names = Fabales_rbcL$speciesname, file.out = "Fabales_rbcL_sequences.fasta")
Fabales_matK <- read.csv("Fabales_matK.csv")
Fabales_matK_genbank_matK <- read.GenBank(Fabales_matK$matk)
write.dna(Fabales_matK_genbank_matK, file = "Fabales_matK.fasta", format = "fasta", append = FALSE)
Fabales_matK_seqinr <- read.fasta(file = "Fabales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Fabales_matK_seqinr, names = Fabales_matK$speciesname, file.out = "Fabales_matK_sequences.fasta")
Fabales_trnH <- read.csv("Fabales_trnH.csv")
Fabales_trnH_genbank_trnH <- read.GenBank(Fabales_trnH$trnh_psba)
write.dna(Fabales_trnH_genbank_trnH, file = "Fabales_trnH.fasta", format = "fasta", append = FALSE)
Fabales_trnH_seqinr <- read.fasta(file = "Fabales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Fabales_trnH_seqinr, names = Fabales_trnH$speciesname, file.out = "Fabales_trnH_sequences.fasta")
Fabales_rbcL <- read.csv("Fabales_rbcL.csv")
Fabales_rbcL_genbank_rbcL <- read.GenBank(Fabales_rbcL$rbcL)
write.dna(Fabales_rbcL_genbank_rbcL, file = "Fabales_rbcL.fasta", format = "fasta", append = FALSE)
Fabales_rbcL_seqinr <- read.fasta(file = "Fabales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Fabales_rbcL_seqinr, names = Fabales_rbcL$speciesname, file.out = "Fabales_rbcL_sequences.fasta")
setwd(dir ="~/Desktop/Order-Wise trees/Ericales")
Ericales_rbcL <- read.csv("Ericales_rbcL.csv")
Ericales_rbcL_genbank_rbcL <- read.GenBank(Ericales_rbcL$rbcL)
write.dna(Ericales_rbcL_genbank_rbcL, file = "Ericales_rbcL.fasta", format = "fasta", append = FALSE)
Ericales_rbcL_seqinr <- read.fasta(file = "Ericales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Ericales_rbcL_seqinr, names = Ericales_rbcL$speciesname, file.out = "Ericales_rbcL_sequences.fasta")
Ericales_matK <- read.csv("Ericales_matK.csv")
Ericales_matK_genbank_matK <- read.GenBank(Ericales_matK$matk)
write.dna(Ericales_matK_genbank_matK, file = "Ericales_matK.fasta", format = "fasta", append = FALSE)
Ericales_matK_seqinr <- read.fasta(file = "Ericales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Ericales_matK_seqinr, names = Ericales_matK$speciesname, file.out = "Ericales_matK_sequences.fasta")
Ericales_trnH <- read.csv("Ericales_trnH.csv")
Ericales_trnH_genbank_trnH <- read.GenBank(Ericales_trnH$trnh_psba)
write.dna(Ericales_trnH_genbank_trnH, file = "Ericales_trnH.fasta", format = "fasta", append = FALSE)
Ericales_trnH_seqinr <- read.fasta(file = "Ericales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Ericales_trnH_seqinr, names = Ericales_trnH$speciesname, file.out = "Ericales_trnH_sequences.fasta")
Ericales_rbcL <- read.csv("Ericales_rbcL.csv")
Ericales_rbcL_genbank_rbcL <- read.GenBank(Ericales_rbcL$rbcL)
write.dna(Ericales_rbcL_genbank_rbcL, file = "Ericales_rbcL.fasta", format = "fasta", append = FALSE)
Ericales_rbcL_seqinr <- read.fasta(file = "Ericales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Ericales_rbcL_seqinr, names = Ericales_rbcL$speciesname, file.out = "Ericales_rbcL_sequences.fasta")
Ericales_matK <- read.csv("Ericales_matK.csv")
Ericales_matK_genbank_matK <- read.GenBank(Ericales_matK$matk)
write.dna(Ericales_matK_genbank_matK, file = "Ericales_matK.fasta", format = "fasta", append = FALSE)
Ericales_matK_seqinr <- read.fasta(file = "Ericales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Ericales_matK_seqinr, names = Ericales_matK$speciesname, file.out = "Ericales_matK_sequences.fasta")
Ericales_trnH <- read.csv("Ericales_trnH.csv")
Ericales_trnH_genbank_trnH <- read.GenBank(Ericales_trnH$trnh_psba)
write.dna(Ericales_trnH_genbank_trnH, file = "Ericales_trnH.fasta", format = "fasta", append = FALSE)
Ericales_trnH_seqinr <- read.fasta(file = "Ericales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Ericales_trnH_seqinr, names = Ericales_trnH$speciesname, file.out = "Ericales_trnH_sequences.fasta")
Ericales_rbcL <- read.csv("Ericales_rbcL.csv")
Ericales_rbcL_genbank_rbcL <- read.GenBank(Ericales_rbcL$rbcL)
write.dna(Ericales_rbcL_genbank_rbcL, file = "Ericales_rbcL.fasta", format = "fasta", append = FALSE)
Ericales_rbcL_seqinr <- read.fasta(file = "Ericales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Ericales_rbcL_seqinr, names = Ericales_rbcL$speciesname, file.out = "Ericales_rbcL_sequences.fasta")
Ericales_matK <- read.csv("Ericales_matK.csv")
Ericales_matK_genbank_matK <- read.GenBank(Ericales_matK$matk)
write.dna(Ericales_matK_genbank_matK, file = "Ericales_matK.fasta", format = "fasta", append = FALSE)
Ericales_matK_seqinr <- read.fasta(file = "Ericales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Ericales_matK_seqinr, names = Ericales_matK$speciesname, file.out = "Ericales_matK_sequences.fasta")
Ericales_trnH <- read.csv("Ericales_trnH.csv")
Ericales_trnH_genbank_trnH <- read.GenBank(Ericales_trnH$trnh_psba)
write.dna(Ericales_trnH_genbank_trnH, file = "Ericales_trnH.fasta", format = "fasta", append = FALSE)
Ericales_trnH_seqinr <- read.fasta(file = "Ericales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Ericales_trnH_seqinr, names = Ericales_trnH$speciesname, file.out = "Ericales_trnH_sequences.fasta")
Ericales_trnH <- read.csv("Ericales_trnH.csv")
Ericales_trnH_genbank_trnH <- read.GenBank(Ericales_trnH$trnh_psba)
write.dna(Ericales_trnH_genbank_trnH, file = "Ericales_trnH.fasta", format = "fasta", append = FALSE)
Ericales_trnH_seqinr <- read.fasta(file = "Ericales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Ericales_trnH_seqinr, names = Ericales_trnH$speciesname, file.out = "Ericales_trnH_sequences.fasta")
library(seqinr)
library(ape)
setwd(dir ="~/Desktop/Order-Wise trees/Fagales")
Fagales_rbcL <- read.csv("Fagales_rbcL.csv")
Fagales_rbcL_genbank_rbcL <- read.GenBank(Fagales_rbcL$rbcL)
write.dna(Fagales_rbcL_genbank_rbcL, file = "Fagales_rbcL.fasta", format = "fasta", append = FALSE)
Fagales_rbcL_seqinr <- read.fasta(file = "Fagales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Fagales_rbcL_seqinr, names = Fagales_rbcL$speciesname, file.out = "Fagales_rbcL_sequences.fasta")
Fagales_matK <- read.csv("Fagales_matK.csv")
Fagales_matK_genbank_matK <- read.GenBank(Fagales_matK$matk)
write.dna(Fagales_matK_genbank_matK, file = "Fagales_matK.fasta", format = "fasta", append = FALSE)
Fagales_matK_seqinr <- read.fasta(file = "Fagales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Fagales_matK_seqinr, names = Fagales_matK$speciesname, file.out = "Fagales_matK_sequences.fasta")
Fagales_trnH <- read.csv("Fagales_trnH.csv")
Fagales_trnH_genbank_trnH <- read.GenBank(Fagales_trnH$trnh_psba)
write.dna(Fagales_trnH_genbank_trnH, file = "Fagales_trnH.fasta", format = "fasta", append = FALSE)
Fagales_trnH_seqinr <- read.fasta(file = "Fagales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Fagales_trnH_seqinr, names = Fagales_trnH$speciesname, file.out = "Fagales_trnH_sequences.fasta")
Fagales_trnH <- read.csv("Fagales_trnH.csv")
Fagales_trnH_genbank_trnH <- read.GenBank(Fagales_trnH$trnh_psba)
write.dna(Fagales_trnH_genbank_trnH, file = "Fagales_trnH.fasta", format = "fasta", append = FALSE)
Fagales_trnH_seqinr <- read.fasta(file = "Fagales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Fagales_trnH_seqinr, names = Fagales_trnH$speciesname, file.out = "Fagales_trnH_sequences.fasta")
Fagales_trnH <- read.csv("Fagales_trnH.csv")
Fagales_trnH_genbank_trnH <- read.GenBank(Fagales_trnH$trnh_psba)
write.dna(Fagales_trnH_genbank_trnH, file = "Fagales_trnH.fasta", format = "fasta", append = FALSE)
Fagales_trnH_seqinr <- read.fasta(file = "Fagales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Fagales_trnH_seqinr, names = Fagales_trnH$speciesname, file.out = "Fagales_trnH_sequences.fasta")
Fagales_rbcL <- read.csv("Fagales_rbcL.csv")
Fagales_rbcL_genbank_rbcL <- read.GenBank(Fagales_rbcL$rbcL)
write.dna(Fagales_rbcL_genbank_rbcL, file = "Fagales_rbcL.fasta", format = "fasta", append = FALSE)
Fagales_rbcL_seqinr <- read.fasta(file = "Fagales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Fagales_rbcL_seqinr, names = Fagales_rbcL$speciesname, file.out = "Fagales_rbcL_sequences.fasta")
r
setwd(dir ="~/Desktop/Order-Wise trees/Gentianales")
Gentianales_rbcL <- read.csv("Gentianales_rbcL.csv")
Gentianales_rbcL_genbank_rbcL <- read.GenBank(Gentianales_rbcL$rbcL)
write.dna(Gentianales_rbcL_genbank_rbcL, file = "Gentianales_rbcL.fasta", format = "fasta", append = FALSE)
Gentianales_rbcL_seqinr <- read.fasta(file = "Gentianales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Gentianales_rbcL_seqinr, names = Gentianales_rbcL$speciesname, file.out = "Gentianales_rbcL_sequences.fasta")
Gentianales_matK <- read.csv("Gentianales_matK.csv")
Gentianales_matK_genbank_matK <- read.GenBank(Gentianales_matK$matk)
write.dna(Gentianales_matK_genbank_matK, file = "Gentianales_matK.fasta", format = "fasta", append = FALSE)
Gentianales_matK_seqinr <- read.fasta(file = "Gentianales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Gentianales_matK_seqinr, names = Gentianales_matK$speciesname, file.out = "Gentianales_matK_sequences.fasta")
Gentianales_trnH <- read.csv("Gentianales_trnH.csv")
Gentianales_trnH_genbank_trnH <- read.GenBank(Gentianales_trnH$trnh_psba)
write.dna(Gentianales_trnH_genbank_trnH, file = "Gentianales_trnH.fasta", format = "fasta", append = FALSE)
Gentianales_trnH_seqinr <- read.fasta(file = "Gentianales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Gentianales_trnH_seqinr, names = Gentianales_trnH$speciesname, file.out = "Gentianales_trnH_sequences.fasta")
Gentianales_rbcL <- read.csv("Gentianales_rbcL.csv")
Gentianales_rbcL_genbank_rbcL <- read.GenBank(Gentianales_rbcL$rbcL)
write.dna(Gentianales_rbcL_genbank_rbcL, file = "Gentianales_rbcL.fasta", format = "fasta", append = FALSE)
Gentianales_rbcL_seqinr <- read.fasta(file = "Gentianales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Gentianales_rbcL_seqinr, names = Gentianales_rbcL$speciesname, file.out = "Gentianales_rbcL_sequences.fasta")
Gentianales_matK <- read.csv("Gentianales_matK.csv")
Gentianales_matK_genbank_matK <- read.GenBank(Gentianales_matK$matk)
write.dna(Gentianales_matK_genbank_matK, file = "Gentianales_matK.fasta", format = "fasta", append = FALSE)
Gentianales_matK_seqinr <- read.fasta(file = "Gentianales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Gentianales_matK_seqinr, names = Gentianales_matK$speciesname, file.out = "Gentianales_matK_sequences.fasta")
Gentianales_trnH <- read.csv("Gentianales_trnH.csv")
Gentianales_trnH_genbank_trnH <- read.GenBank(Gentianales_trnH$trnh_psba)
write.dna(Gentianales_trnH_genbank_trnH, file = "Gentianales_trnH.fasta", format = "fasta", append = FALSE)
Gentianales_trnH_seqinr <- read.fasta(file = "Gentianales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Gentianales_trnH_seqinr, names = Gentianales_trnH$speciesname, file.out = "Gentianales_trnH_sequences.fasta")
Gentianales_rbcL <- read.csv("Gentianales_rbcL.csv")
Gentianales_rbcL_genbank_rbcL <- read.GenBank(Gentianales_rbcL$rbcL)
write.dna(Gentianales_rbcL_genbank_rbcL, file = "Gentianales_rbcL.fasta", format = "fasta", append = FALSE)
Gentianales_rbcL_seqinr <- read.fasta(file = "Gentianales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Gentianales_rbcL_seqinr, names = Gentianales_rbcL$speciesname, file.out = "Gentianales_rbcL_sequences.fasta")
Gentianales_trnH <- read.csv("Gentianales_trnH.csv")
Gentianales_trnH_genbank_trnH <- read.GenBank(Gentianales_trnH$trnh_psba)
write.dna(Gentianales_trnH_genbank_trnH, file = "Gentianales_trnH.fasta", format = "fasta", append = FALSE)
Gentianales_trnH_seqinr <- read.fasta(file = "Gentianales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Gentianales_trnH_seqinr, names = Gentianales_trnH$speciesname, file.out = "Gentianales_trnH_sequences.fasta")
Gentianales_rbcL <- read.csv("Gentianales_rbcL.csv")
Gentianales_rbcL_genbank_rbcL <- read.GenBank(Gentianales_rbcL$rbcL)
write.dna(Gentianales_rbcL_genbank_rbcL, file = "Gentianales_rbcL.fasta", format = "fasta", append = FALSE)
Gentianales_rbcL_seqinr <- read.fasta(file = "Gentianales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Gentianales_rbcL_seqinr, names = Gentianales_rbcL$speciesname, file.out = "Gentianales_rbcL_sequences.fasta")
setwd(dir ="~/Desktop/Order-Wise trees/Lamiales")
Lamiales_rbcL <- read.csv("Lamiales_rbcL.csv")
Lamiales_rbcL_genbank_rbcL <- read.GenBank(Lamiales_rbcL$rbcL)
write.dna(Lamiales_rbcL_genbank_rbcL, file = "Lamiales_rbcL.fasta", format = "fasta", append = FALSE)
Lamiales_rbcL_seqinr <- read.fasta(file = "Lamiales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Lamiales_rbcL_seqinr, names = Lamiales_rbcL$speciesname, file.out = "Lamiales_rbcL_sequences.fasta")
Lamiales_matK <- read.csv("Lamiales_matK.csv")
Lamiales_matK_genbank_matK <- read.GenBank(Lamiales_matK$matk)
write.dna(Lamiales_matK_genbank_matK, file = "Lamiales_matK.fasta", format = "fasta", append = FALSE)
Lamiales_matK_seqinr <- read.fasta(file = "Lamiales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Lamiales_matK_seqinr, names = Lamiales_matK$speciesname, file.out = "Lamiales_matK_sequences.fasta")
Lamiales_trnH <- read.csv("Lamiales_trnH.csv")
Lamiales_trnH_genbank_trnH <- read.GenBank(Lamiales_trnH$trnh_psba)
write.dna(Lamiales_trnH_genbank_trnH, file = "Lamiales_trnH.fasta", format = "fasta", append = FALSE)
Lamiales_trnH_seqinr <- read.fasta(file = "Lamiales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Lamiales_trnH_seqinr, names = Lamiales_trnH$speciesname, file.out = "Lamiales_trnH_sequences.fasta")
setwd(dir ="~/Desktop/Order-Wise trees/Laurales")
Laurales_rbcL <- read.csv("Laurales_rbcL.csv")
Laurales_rbcL_genbank_rbcL <- read.GenBank(Laurales_rbcL$rbcL)
write.dna(Laurales_rbcL_genbank_rbcL, file = "Laurales_rbcL.fasta", format = "fasta", append = FALSE)
Laurales_rbcL_seqinr <- read.fasta(file = "Laurales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Laurales_rbcL_seqinr, names = Laurales_rbcL$speciesname, file.out = "Laurales_rbcL_sequences.fasta")
Laurales_matK <- read.csv("Laurales_matK.csv")
Laurales_matK_genbank_matK <- read.GenBank(Laurales_matK$matk)
write.dna(Laurales_matK_genbank_matK, file = "Laurales_matK.fasta", format = "fasta", append = FALSE)
Laurales_matK_seqinr <- read.fasta(file = "Laurales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Laurales_matK_seqinr, names = Laurales_matK$speciesname, file.out = "Laurales_matK_sequences.fasta")
Laurales_trnH <- read.csv("Laurales_trnH.csv")
Laurales_trnH_genbank_trnH <- read.GenBank(Laurales_trnH$trnh_psba)
write.dna(Laurales_trnH_genbank_trnH, file = "Laurales_trnH.fasta", format = "fasta", append = FALSE)
Laurales_trnH_seqinr <- read.fasta(file = "Laurales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Laurales_trnH_seqinr, names = Laurales_trnH$speciesname, file.out = "Laurales_trnH_sequences.fasta")
Lamiales_trnH <- read.csv("Lamiales_trnH.csv")
Lamiales_trnH_genbank_trnH <- read.GenBank(Lamiales_trnH$trnh_psba)
write.dna(Lamiales_trnH_genbank_trnH, file = "Lamiales_trnH.fasta", format = "fasta", append = FALSE)
Lamiales_trnH_seqinr <- read.fasta(file = "Lamiales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Lamiales_trnH_seqinr, names = Lamiales_trnH$speciesname, file.out = "Lamiales_trnH_sequences.fasta")
setwd(dir ="~/Desktop/Order-Wise trees/Lamiales")
Lamiales_trnH <- read.csv("Lamiales_trnH.csv")
Lamiales_trnH_genbank_trnH <- read.GenBank(Lamiales_trnH$trnh_psba)
write.dna(Lamiales_trnH_genbank_trnH, file = "Lamiales_trnH.fasta", format = "fasta", append = FALSE)
Lamiales_trnH_seqinr <- read.fasta(file = "Lamiales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Lamiales_trnH_seqinr, names = Lamiales_trnH$speciesname, file.out = "Lamiales_trnH_sequences.fasta")
setwd(dir ="~/Desktop/Order-Wise trees/Magnoliales")
Magnoliales_rbcL <- read.csv("Magnoliales_rbcL.csv")
Magnoliales_rbcL_genbank_rbcL <- read.GenBank(Magnoliales_rbcL$rbcL)
write.dna(Magnoliales_rbcL_genbank_rbcL, file = "Magnoliales_rbcL.fasta", format = "fasta", append = FALSE)
Magnoliales_rbcL_seqinr <- read.fasta(file = "Magnoliales_rbcL.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Magnoliales_rbcL_seqinr, names = Magnoliales_rbcL$speciesname, file.out = "Magnoliales_rbcL_sequences.fasta")
Magnoliales_matK <- read.csv("Magnoliales_matK.csv")
Magnoliales_matK_genbank_matK <- read.GenBank(Magnoliales_matK$matk)
write.dna(Magnoliales_matK_genbank_matK, file = "Magnoliales_matK.fasta", format = "fasta", append = FALSE)
Magnoliales_matK_seqinr <- read.fasta(file = "Magnoliales_matK.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Magnoliales_matK_seqinr, names = Magnoliales_matK$speciesname, file.out = "Magnoliales_matK_sequences.fasta")
Magnoliales_trnH <- read.csv("Magnoliales_trnH.csv")
Magnoliales_trnH_genbank_trnH <- read.GenBank(Magnoliales_trnH$trnh_psba)
write.dna(Magnoliales_trnH_genbank_trnH, file = "Magnoliales_trnH.fasta", format = "fasta", append = FALSE)
Magnoliales_trnH_seqinr <- read.fasta(file = "Magnoliales_trnH.fasta", seqtype = "DNA", as.string = TRUE, forceDNAtolower = FALSE)
write.fasta(sequences = Magnoliales_trnH_seqinr, names = Magnoliales_trnH$speciesname, file.out = "Magnoliales_trnH_sequences.fasta")
