常用生信软件安装使用

非必要，不选择添加环境变量；直接路径+命令

1.MUSCLE 5.1

1.1下载

wget https://github.com/rcedgar/muscle/releases/download/5.1.0/muscle5.1.linux_intel64

1.2给予权限

chmod +x /usr/bin/muscle5.1.linux_intel64
#/usr/bin/ 安装的路径
#muscle5.1.linux_intel64 软件名称，
#可以更改，例如muscle5，不影响使用

1.3基本使用

/usr/bin/muscle5.0.98_linux -align seqs.fa -output aln.afa
#/usr/bin/muscle5.0.98_linux
使用必须要路径，也就是/usr/bin/  路径+软件名
#seqs.fa
要处理的文件
#aln.afa
输出的文件

2.FastTtree2.1

2.1下载

#下载

wget http://www.microbesonline.org/fasttree/FastTree

2.2权限

chmod +x /usr/bin/FastTree
#/usr/bin/ 安装的路径

2.3使用

路径名称+ 命令

FastTree要求输入的多序列比对结果为FASTA或者Phylip格式，对于蛋白质的进化树构建，基本用法如下

FastTree protein.fasta > tree

也可以选择LG或者WAG替换模型，用法如下

FastTree -lg protein.fasta > tree
FastTree -wag protein.fasta > tree

对于核酸序列，基本用法如下

FastTree -nt nucleotide.fasta > tree

也可以选择GTR替换模型，用法如下

FastTree -nt  -gtr nucleotide.fasta > tree

默认生成的tree 文件是 Newick格式， 可以导入 figTree 或者 TreeViewer等软件中进行查看。

ps：用MUSCLE比对的文件进行跑，而不是直接序列文件；

生成的tree文件格式类似如下：

(Av4b01g40.t1:0.55178,Av4b01g10.t1:0.57274,(Av4b01g80.t1:0.29000,(Av4b01g30.t1:0.44773,(Av4b01g000050.t1:0.48835,(Av4b01g20.t1:0.36315,(Av4b01g60.t1:0.43676,Av4b01g70.t1:0.46517)0.956:0.20063)0.596:0.11173)0.540:0.05168)0.998:0.32048)0.742:0.05555);

最简单的树形结构

在线可视化网址：https://itol.embl.de/

3.CLUSTALW

1.下载使用与MUSCLE一样

2.基本使用

#命令1.选择比对的类型
/root/clustalw2/clustalw2 two.fasta -type=dna
    -TYPE=       :PROTEIN or DNA sequences
#命令2.输出格式
/root/clustalw2/clustalw2 two.fasta -output=PHYLIP
-OUTPUT=     :CLUSTAL(default), GCG, GDE, PHYLIP, PIR, NEXUS and FASTA

4.MEME 下载使用

4.1下载

wget https://meme-suite.org/meme/meme-software/5.5.5/meme-5.5.5.tar.gz

4.2安装

#安装命令来自官网，我安装没问题
tar zxf meme-5.5.5.tar.gz
cd meme-5.5.5
./configure --prefix=$HOME/meme --enable-build-libxml2 --enable-build-libxslt
make
make test
make install
export PATH=$HOME/meme/bin:$HOME/meme/libexec/meme-5.5.5:$PATH 


#成功之后
[root~]# meme
 Usage:	meme	<dataset> [optional arguments]

	<dataset> 		file containing sequences in FASTA format
	[-h]			print this message
	[-o <output dir>]	name of directory for output files
				will not replace existing directory
	[-oc <output dir>]	name of directory for output files
				will replace existing directory
	[-text]			output in text format (default is HTML)
	[-objfun classic|de|se|cd|ce]	objective function (default: classic)
	[-test mhg|mbn|mrs]	statistical test type (default: mhg)
	[-use_llr]		use LLR in search for starts in Classic mode
	[-neg <negdataset>]	file containing control sequences
	[-shuf <kmer>]		preserve frequencies of k-mers of size <kmer> 
				when shuffling (default: 2)
	[-hsfrac <hsfrac>]	fraction of primary sequences in holdout set 
				(default: 0.5)
	[-cefrac <cefrac>]	fraction sequence length for CE region 
				(default: 0.25)
	[-searchsize <ssize>]	maximum portion of primary dataset to use
				for motif search (in characters)
	[-maxsize <maxsize>]	maximum dataset size in characters
	[-norand]		do not randomize the order of the input 
				sequences with -searchsize
	[-csites <csites>]	maximum number of sites for EM in Classic mode
	[-seed <seed>]		random seed for shuffling and sampling
	[-dna]			sequences use DNA alphabet
	[-rna]			sequences use RNA alphabet
	[-protein]		sequences use protein alphabet
	[-alph <alph file>]	sequences use custom alphabet
	[-revcomp]		allow sites on + or - DNA strands
	[-pal]			force palindromes (requires -dna)
	[-mod oops|zoops|anr]	distribution of motifs
	[-nmotifs <nmotifs>]	maximum number of motifs to find
	[-evt <ev>]		stop if motif E-value greater than <evt>
	[-time <t>]		quit before <t> seconds have elapsed
	[-nsites <sites>]	number of sites for each motif
	[-minsites <minsites>]	minimum number of sites for each motif
	[-maxsites <maxsites>]	maximum number of sites for each motif
	[-wnsites <wnsites>]	weight on expected number of sites
	[-w <w>]		motif width
	[-minw <minw>]		minimum motif width
	[-maxw <maxw>]		maximum motif width
	[-allw]			test starts of all widths from minw to maxw
	[-nomatrim]		do not adjust motif width using multiple
				alignment
	[-wg <wg>]		gap opening cost for multiple alignments
	[-ws <ws>]		gap extension cost for multiple alignments
	[-noendgaps]		do not count end gaps in multiple alignments
	[-bfile <bfile>]	name of background Markov model file
	[-markov_order <order>]	(maximum) order of Markov model to use or create
	[-psp <pspfile>]	name of positional priors file
	[-maxiter <maxiter>]	maximum EM iterations to run
	[-distance <distance>]	EM convergence criterion
	[-prior dirichlet|dmix|mega|megap|addone]
				type of prior to use
	[-b <b>]		strength of the prior
	[-plib <plib>]		name of Dirichlet prior file
	[-spfuzz <spfuzz>]	fuzziness of sequence to theta mapping
	[-spmap uni|pam]	starting point seq to theta mapping type
	[-cons <cons>]		consensus sequence to start EM from
	[-brief <n>]		omit sites and sequence tables in
				output if more than <n> primary sequences
	[-nostatus]		do not print progress reports to terminal
	[-p <np>]		use parallel version with <np> processors
	[-sf <sf>]		print <sf> as name of sequence file
	[-V]			verbose mode
	[-version]		display the version number and exit

5.源码安装circos；GD模块出错解决方案；

一般来说，为了方便可以直接只用conda 安装circos；

 5.1circos 模块缺失

#circos/bin/circos  -module #这是我自己的命令查看命令；你自己查看模块；按照教程来
#有时间我会将整个安装过程补充；

missing            GD
missing            GD::Polyline

如果其他模块缺失；可以使用 cpan -i  SVG #cpan -i 缺失模块名

5.2GD模块缺失解决;看了几个解决方案，一般说是缺少libgd库；

因为我的系统是ubuntu，因为我是root权限所以为了省事直接apt-get install

sudo apt-get update #更新一下
sudo apt-get install libgd-dev#安装 libgd-dev库

安装完成之后

cpan -i GD

cpan -i GD::Polyline


#非root 权限参考以下操作；别人的解决方案

解决办法：安装libgd库 安装路径/public/home/xiayy/softWare/current/bin下面解压安装
wget https://github.com/libgd/libgd/releases/download/gd-2.2.5/libgd-2.2.5.tar.gz
tar zxvf libgd-2.2.5.tar.gz
cd libgd-2.2.5
./ configure -prefix =/home/xiayy/softWare/circos-0.69 （此处非root用户，或者只是在自己目录下有效）
make
make install
make installcheck
12.然后再去安装两个GD模块：
cpan[1]> install GD.pm
cpan[2]> install GD::Polyline
cpan[3]> reload cpan
cpan[4]> exit


好像centos7.6没有这个问题