1. PHYLIP简介

PHYLIP,the Phylogeny Inference Package, is a package of programs for inferring phylogenies (evolutionary trees). It can infer phylogenies by parsimony, compatibility, distance matrix methods, and likelihood. It can also compute consensus trees, compute distances between trees, draw trees, resample data sets by bootstrapping or jackknifing, edit trees, and compute distance matrices. It can handle data that are nucleotide sequences, protein sequences, gene frequencies, restriction sites, restriction fragments, distances, discrete characters, and continuous characters.

2. PHYLIP的下载和安装

下载PHYLIP，然后解压缩，得到phylip的安装文件包，其中包含doc、exe和src三个文件夹以及一个phylip.html文件。html文件结合doc中的文件在浏览器中打开是phylip详细的说明文件。当然，官网也提供了phylip 3.6的PDF版的Manual文件。

$ wget http://evolution.gs.washington.edu/phylip/download/phylip-3.695.tar.gz
$ tar zxf phylip-3.695.tar.gz -C /opt/biosoft/
$ cd /opt/biosoft/phylip-3.695/src/
$ cp Makefile.unx Makefile
$ make install