Building Muscle 5.1.osx-arm64

近日想构建一个进化树，需要用到几个软件。参考了白洋组之前发表在《遗传》杂志上的一篇小综述，决定安装一下MSULE，目前版本为5.1。

Introduction of MUSCLE-v5.1

Application
Most popular bioinformatics-software for Multiple Sequence Alignment(also known as MSA).

Advantage
Highest accuracy, scalable to thousands of sequences

Compared to previous versions, Muscle v5 is much more accurate, is often faster, and scales to much larger datasets. At the time of writing (late 2021), Muscle v5 has the highest scores on multiple alignment benchmarks including Balibase, Bralibase, Prefab and Balifam. It can align tens of thousands of sequences with high accuracy on a low-cost commodity computer (say, an 8-core Intel CPU with 32 Gb RAM). On large datasets, Muscle v5 is 20-30% more accurate than MAFFT and Clustal-Omega
(https://www.drive5.com/muscle/)

Download

Mac配置：macOS Monterey（Version 12.0.1）

github 上有相应的安装包和教程，具体操作如下：

#按照教程上所说的“Note that in recent releases of OSX, "gcc" is an alias for clang. You must install genuine gcc v11 and its OpenMP library; currently brew install gcc does this.”
#我们需要先安装好gcc v11，使用brew安装
#由于我之前已经安装过了，所以直接：
brew install gcc

#在这里报错了，显示：
==> Searching for similarly named formulae...
Error: No similarly named formulae found.
Error: No available formula or cask with the name "htop".
==> Searching for a previously deleted formula (in the last month)...
Error: No previously deleted formula found.
==> Searching taps on GitHub...
Error: No formulae found in taps.

参考了几种解决方法以后，发现原来是因为之前homebrew安装时，只安装了源代码仓库 brew，却没有安装核心源 homebrew-core[1] [2] [3] [4] . 于是在终端中进行如下操作：

#安装homebrew-core
cd "$(brew --repo)/Library/Taps/"
mkdir homebrew && cd homebrew
git clone git://mirrors.ustc.edu.cn/homebrew-core.git
#接着再更新一下
brew update
#Bingo！

接着回来继续安装gcc v11

brew install gcc

#2.下载源码到目标文件夹 ～/biosoft，解压缩
mkdir ~/biosoft ;cd ~/biosoft
wget https://github.com/rcedgar/muscle/archive/refs/tags/v5.1.tar.gz
tar -xvzf v5.1.tar.gz
cd muscle-5.1/src
make
#在我的电脑里，安装在了../src路径下的Darwin文件夹中。
cd Darwin; ls -l
#此处可以看到muscle 为执行文件
#接着需要再验证一下是否安装成功：
muscle -- version

至此，就已经安装好了。

此外，可以将muscle写入环境变量中，便于直接muscle就可以调用。（macOS中配置文件located at ~/.zshrc.）