1. 介绍

2. 使用

2.1 下载

  1. $ conda search muscle
  2. Loading channels: done
  3. # Name                       Version           Build  Channel
  4. muscle                        3.8.31               0  bioconda
  5. muscle                      3.8.1551               1  bioconda
  6. muscle                      3.8.1551               2  bioconda
  7. muscle                      3.8.1551      h2d50403_3  bioconda
  8. muscle                      3.8.1551      h6bb024c_4  bioconda
  9. muscle                      3.8.1551      h7d875b9_6  bioconda
  10. muscle                      3.8.1551      hc9558a2_5  bioconda
  11. muscle                           5.1      h7d875b9_0  bioconda
  12. muscle                           5.1      h9f5acd7_1  bioconda

2.2 运行

  1. $ cat test.fa
  2. >gene1
  3. MRLFLLLAFNALMQLEAYGFTDESDRQALLEIKSQVSESKRDALSAWNNSFP
  4. >gene2
  5. MGVPCIVMRLILVSALLVSVSLEHSDMVCAQTIRLTEETDKQALLEFKETSRVVLG
  6. >gene3
  7. MRLFLLLAFNALMLLETHGFTDETDRQALLQFKSQVSEDKRVVLSSWNHSFPLCNWKGVT
  8. >gene4
  9. MKLFLLLSFSAHLLLGETDRQALLEFKSQVSEGKRDVLSSWNNSFPLCNWKWVT
  10. >gene5
  11. MKLSFSLVFNALTLLLQVCIFAQARFSNETDMQALLEFKSQVSENNKREVLASWNHSSPF
  12. >gene6
  13. MKVCILVFAQARFSNETDMQALLEFKSQVTENKREVLASWNHSFPL
  1. $ muscle -in test.fa -quiet | seqkit seq -w 0
  2. >gene2
  3. MGVPCIVMRLILVSALLVSVSLEHSDMVCAQTIRLTEETDKQALLEFKE-----TSRVVLG---------------
  4. >gene5
  5. -------MKLSFS--LVFNALTLLLQVCIFAQARFSNETDMQALLEFKSQVSENNKREVLASWNHSSPF-------
  6. >gene6
  7. -------MKVCIL---------------VFAQARFSNETDMQALLEFKSQVTE-NKREVLASWNHSFPL-------
  8. >gene4
  9. -------MKLFLL--LSFSAHL------LL------GETDRQALLEFKSQVSE-GKRDVLSSWNNSFPLCNWKWVT
  10. >gene1
  11. -------MRLFLL--LAFNALM------QLEAYGFTDESDRQALLEIKSQVSE-SKRDALSAWNNSFP--------
  12. >gene3
  13. -------MRLFLL--LAFNALM------LLETHGFTDETDRQALLQFKSQVSE-DKRVVLSSWNHSFPLCNWKGVT
  • 其他

看来我的版本比较老了

  1. $ muscle
  3. MUSCLE v3.8.1551 by Robert C. Edgar
  5. http://www.drive5.com/muscle
  6. This software is donated to the public domain.
  7. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.
  10. Basic usage
  12.     muscle -in <inputfile> -out <outputfile>
  14. Common options (for a complete list please see the User Guide):
  16.     -in <inputfile>    Input file in FASTA format (default stdin)
  17.     -out <outputfile>  Output alignment in FASTA format (default stdout)
  18.     -diags             Find diagonals (faster for similar sequences)
  19.     -maxiters <n>      Maximum number of iterations (integer, default 16)
  20.     -maxhours <h>      Maximum time to iterate in hours (default no limit)
  21.     -html              Write output in HTML format (default FASTA)
  22.     -msf               Write output in GCG MSF format (default FASTA)
  23.     -clw               Write output in CLUSTALW format (default FASTA)
  24.     -clwstrict         As -clw, with 'CLUSTAL W (1.81)' header
  25.     -log[a] <logfile>  Log to file (append if -loga, overwrite if -log)
  26.     -quiet             Do not write progress messages to stderr
  27.     -version           Display version information and exit
  29. Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2
  30. Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3
  31. Fastest possible (nucleotides): -maxiters 1 -diags

参考

在线：https://www.ebi.ac.uk/Tools/msa/muscle/

本地：https://www.drive5.com/muscle/

多序列比对的软件：muscle、mafft、clustalw……
现在常用的是前两者，上面用的mafft，这里看一下muscle

什么时候要用到多序列比对，它的结果能用于什么呢？

  1. 用于构建基因树：
    1.1 用trimAl 修剪比对结果，用iqtree、fasttree等进行建pep树；
    1.2 用pal2nal.pl将cds序列回帖到比对结果，用于构建cds树。
  2. 用于构建物种树：将单拷贝基因家族的比对结果串联建树。
  3. 共线性块上的基因对进行全局比对，回帖cds序列，用yn00等计算ka、ks值。

如果不正确，希望批评指正！