官网：http://provean.jcvi.org/index.php

1、从README（http://provean.jcvi.org/downloads/README）可知，需要下载以下软件和数据库
（1） NCBI BLAST 2.4.0
Index of /blast/executables/blast+/2.4.0

（2） CD-HIT 3.1.2 (or more recent, but currently v4.6 and v4.6.1 are not recommended since those versions have a reported problem,
https://code.google.com/p/cdhit/issues/detail?id=18)

[Releases · weizhongli/cdhit](https://github.com/weizhongli/cdhit/releases)找到适合的版本下载

wget -c https://github.com/weizhongli/cdhit/releases/download/V4.8.1/cd-hit-v4.8.1-2019-0228.tar.gz

tar -zxvf cd-hit-v4.8.1-2019-0228.tar.gz

cd cd-hit-v4.8.1-2019-0228
make

cp cd-hit ~/bin

（3） NCBI nr (non-redundant) protein database

#!/bin/bash

for I in {000..116}
do
        wget https://ftp.ncbi.nih.gov/blast/db/nr.${I}.tar.gz
        wget https://ftp.ncbi.nih.gov/blast/db/nr.${I}.tar.gz.md5
done

#tar解压

2、下载PROVEAN，wget无法访问网址，需挂梯子，也可以下载到电脑上，再传到服务器中

3、安装PROVEAN

tar -zxvf provean-1.1.5.tar.gz

cd provean-1.1.5
 ./configure BLAST_DB=/path/to/blast/database/nr        #nr数据库所在路径 / 数据库名称（很重要）
make        #报错，再次make即可
make install        #提示无权限，加sudo解决

provean.sh -h        #成功安装
PROVEAN v1.1.5

USAGE:
  provean.sh [Options]

Example:
 # Given a query sequence in aaa.fasta file, 
 # compute scores for variations in bbb.var file 
 provean.sh -q aaa.fasta -v bbb.var

Required arguments:
 -q <string>, --query <string>
   Query protein sequence filename in fasta format
 -v <string>, --variation <string>
   Variation filename containing a list of variations:
     one entry per line in HGVS notation,
     e.g.: G105C, F508del, Q49dup, Q49_P50insC, Q49_R52delinsLI

Optional arguments:
 --save_supporting_set <string>
   Saves supporting sequence set infomation into a given filename
 --supporting_set <string>
   Supporting sequence set filename saved with '--save_supporting_set' option above
   (This will save time for BLAST search and clustering.)
 --tmp_dir <string>
   Temporary directory used to store temporary files
 --num_threads <integer>
   Number of threads (CPUs) to use in BLAST search
 -V, --verbose
   Verbosely shows the information about procedure
 -h, --help
   Gives this help message