之前一直用的是muscle，看到一个文章使用了Kalign，尝试一下吧

安装

wget -c https://github.com/TimoLassmann/kalign/archive/refs/tags/v3.4.0.tar.gz
tar -zxvf v3.4.0.tar.gz
cd kalign-3.4.0
mkdir build 
cd build
cmake .. 
make 
make test 
sudo make install

 用法

Usage: kalign  -i <seq file> -o <out aln>--type:       Alignment type (rna, dna, internal). [rna]Options: protein, divergent (protein) rna, dna, internal (nuc). 
-n/--nthreads:Number of threads. [4]