V.PhyloMaker,R软件包,用于生成维管束植物的系统发育树。V.PhyloMaker中实现的巨型树(即GBOTB.extended.tre),包括现存维管植物的74 533个物种和所有科,拥有较为完整的维管植物系统发育框架。V.PhyloMaker可以为非常大的物种列表生成系统发育(测试的最大物种列表包括314 686个物种)。
链接: V.PhyloMaker: an R package that can generate very large phylogenies for vascular plants.
library("picante")
library("V.PhyloMaker")
library("plantlist")
data<- read.table("C:/Users/HUAWEI/Desktop/xxx.csv", header = TRUE, sep = "\t", row.names = 1)
species_list <- rownames(data)
sp_lis <- subset(TPL(species_list),select = c("YOUR_SEARCH", "POSSIBLE_GENUS", "FAMILY"))
colnames(sp_lis) <- c("species", "genus", "family")
sp_tree <- phylo.maker(sp.lis=sp_lis) #
sp_tr <- sp_tree$scenario.3
write.tree(sp_tr, "D:/xxx.tre")
Jin, Y., & Qian, H. (2019). V. PhyloMaker: an R package that can generate very large phylogenies for vascular plants. Ecography, 42(8), 1353-1359.