用 phylomatic 软件生成的进化树

用 phylomatic 软件生成的进化树

Phylomatic是在线软件，可以利用植物名录，按照APGIII的被子植物科的拓扑结构，生成进化树。

########## 参考 张金龙博士

工作目录

setwd("E:\\my_research\\my_scripts\\植物转录组发育进化树")

安装 plantlist

install.packages("E:/my_research/my_scripts/植物转录组发育进化树/plantlist_0.0.12.zip", repos = NULL)

引用信息 plantlist_0.0.12.zip http://blog.sciencenet.cn/home.php?mod=space&uid=255662&do=blog&id=816837

plantlist 的依赖包

library(openxlsx)
library(plantlist)

导入查询物种

# preparation
cat splist.csv
Abelmoschus esculentus
Abies alba
Abies balsamea
Acacia aulacocarpa
...
sed 'H;$!d;${x;s/^\n/"/;s/\n/","/g;s/$/"/}' splist.csv > splist
"Abelmoschus esculentus","Abies alba","Abies balsamea","Acacia aulacocarpa"...

---

splist <- c("Abelmoschus esculentus","Abies alba","Abies balsamea","Acacia aulacocarpa","Acacia mangium","Acacia senegal","Acacia victoriae","Acrocarpus fraxinifolius","Adansonia digitata","Agave deserti","Agave tequilana","Albizia lebbeck","Allium cepa","Allium sativum","Ammopiptanthus mongolicus","Amorphophallus bulbifer","Amorphophallus konjac","Amsonia hubrichtii","Ananas comosus","Andrographis paniculata","Apium graveolens","Argemone mexicana","Arnica chamissonis","Arnica montana","Artemisia absinthium","Artemisia chamaemelifolia","Artemisia maritima","Asparagus officinalis","Aspidistra saxicola","Atropa belladonna","Berberis thunbergii","Bituminaria bituminosa","Boehmeria nivea","Bupleurum chinense","Calliandra calothyrsus")

查询物种所在的科属

res <- TPL(splist)

生成科属种列表， 该列表可以用于Phylomatic (http://phylodiversity.net/phylomatic/)软件生成进化树用

Phylomatic 教程 (http://blog.sciencenet.cn/blog-807429-634316.html)

Species_list <- taxa.table(res)

CTPL函数 指定中文名， 生成对应的科属种和学名列表

write.csv(Species_list, "PlantransDB_list.csv")

Phylomatic (v3)

将 PlantransDB_list.csv 中物种的科属种全部粘贴到 http://phylodiversity.net/phylomatic/ 中 “taxa=” 对应的框内，

storedtree = R20120829 (Phylomatic tree R20120829 for plants), clean = true

点击 send 即可生成 newick 格式的进化树

将在phylomatic 中生成的树用 Fig Tree v1.4.0 处理