近日想構(gòu)建一個(gè)進(jìn)化樹炒嘲，需要用到幾個(gè)軟件。參考了白洋組之前發(fā)表在《遺傳》雜志上的一篇小綜述，決定安裝一下MSULE隘击，目前版本為5.1替久。
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 sequencesCompared 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 上有相應(yīng)的安裝包和教程，具體操作如下：
#按照教程上所說的“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.”
#我們需要先安裝好gcc v11辫呻，使用brew安裝
#由于我之前已經(jīng)安裝過了清钥，所以直接：
brew install gcc
#在這里報(bào)錯(cuò)了，顯示：
==> 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.
參考了幾種解決方法以后放闺，發(fā)現(xiàn)原來是因?yàn)橹癶omebrew安裝時(shí)祟昭，只安裝了源代碼倉(cāng)庫 brew，卻沒有安裝核心源 homebrew-core[1] [2] [3] [4] . 于是在終端中進(jìn)行如下操作：
#安裝homebrew-core
cd "$(brew --repo)/Library/Taps/"
mkdir homebrew && cd homebrew
git clone git://mirrors.ustc.edu.cn/homebrew-core.git
#接著再更新一下
brew update
#Bingo怖侦！
接著回來繼續(xù)安裝gcc v11
brew install gcc
#2.下載源碼到目標(biāo)文件夾 ～/biosoft篡悟，解壓縮
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
#在我的電腦里，安裝在了../src路徑下的Darwin文件夾中匾寝。
cd Darwin; ls -l
#此處可以看到muscle 為執(zhí)行文件
#接著需要再驗(yàn)證一下是否安裝成功：
muscle -- version
至此搬葬，就已經(jīng)安裝好了。
此外艳悔，可以將muscle寫入環(huán)境變量中踩萎，便于直接muscle就可以調(diào)用。（macOS中配置文件located at ~/.zshrc.）
