RAxML

1. 安装 RAxML

从 github 仓库克隆代码安装。

$ git clone https://github.com/stamatak/standard-RAxML
$ cd standard-RAxML
$ make -f Makefile.SSE3.PTHREADS.gcc && rm *.o
$ sudo ln -s `pwd`/raxmlHPC-PTHREADS-SSE3 /usr/local/bin/raxml

2. 使用 RAxML

# 绘制无根树
$ raxml -s alignment.phy -m GTRGAMMA -p 12345 -T 40 -w raxml_output -n raxml
# 绘制有跟树，如根名叫 xyz
$ raxml -s alignment.phy -m GTRGAMMA -p 12345 -o xyz

3. Reference

• http://sco.h-its.org/exelixis/resource/doc/Phylo100225.pdf