muscle只能在Linux上运行，下面是下载和使用，参考自官网http://www.drive5.com/muscle/manual/install.html
- 下载http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
- 用filezila传到服务器上
- 解压tar zxvf muscle3.8.31_i86linux64.tar.gz，不用编译，解压后要修改权限
- 修改权限，chmod +x /home/donglm/Dlm_wk/asemb_assess/software/muscle3.8.31_i86linux64，否则会被deny
- 可以使用了：/home/donglm/Dlm_wk/asemb_assess/software/muscle3.8.31_i86linux64 -in /home/donglm/Dlm_wk/asemb_assess/seq/larch_prot.fasta -out /home/donglm/Dlm_wk/asemb_assess/seq/larch_prot_align.fasta
运行信息：
MUSCLE v3.8.31 by Robert C. Edgar
http://www.drive5.com/muscle
This software is donated to the public domain.
Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.
larch_prot 28 seqs, max length 483, avg length 221
00:00:00 10 MB(-3%) Iter 1 100.00% K-mer dist pass 1
00:00:00 10 MB(-3%) Iter 1 100.00% K-mer dist pass 2
00:00:00 17 MB(-5%) Iter 1 100.00% Align node
00:00:00 17 MB(-5%) Iter 1 100.00% Root alignment
00:00:00 17 MB(-5%) Iter 2 100.00% Refine tree
00:00:00 17 MB(-5%) Iter 2 100.00% Root alignment
00:00:00 17 MB(-5%) Iter 2 100.00% Root alignment
00:00:00 17 MB(-5%) Iter 3 100.00% Refine biparts
00:00:00 17 MB(-5%) Iter 4 100.00% Refine biparts
00:00:00 17 MB(-5%) Iter 5 100.00% Refine biparts
00:00:00 17 MB(-5%) Iter 5 100.00% Refine biparts
00:00:00 17 MB(-5%) Iter 6 100.00% Refine biparts
00:00:01 17 MB(-5%) Iter 7 100.00% Refine biparts
00:00:01 17 MB(-5%) Iter 8 100.00% Refine biparts
00:00:01 17 MB(-5%) Iter 9 100.00% Refine biparts
00:00:01 17 MB(-5%) Iter 9 100.00% Refine biparts
