MSA - multi sequence alignment

Muscle  -  Link1  Link2  Link3

Usage:

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.


Basic usage

    muscle -in <inputfile> -out <outputfile>

Common options (for a complete list please see the User Guide):

    -in <inputfile>    Input file in FASTA format (default stdin)
    -out <outputfile>  Output alignment in FASTA format (default stdout)
    -diags             Find diagonals (faster for similar sequences)
    -maxiters <n>      Maximum number of iterations (integer, default 16)
    -maxhours <h>      Maximum time to iterate in hours (default no limit)
    -html              Write output in HTML format (default FASTA)
    -msf               Write output in GCG MSF format (default FASTA)
    -clw               Write output in CLUSTALW format (default FASTA)
    -clwstrict         As -clw, with 'CLUSTAL W (1.81)' header
    -log[a] <logfile>  Log to file (append if -loga, overwrite if -log)
    -quiet             Do not write progress messages to stderr
    -version           Display version information and exit

Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2
Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3
Fastest possible (nucleotides): -maxiters 1 -diags

T_Coffee  -  Link1  Link2  Link3

T-Coffee (中文直翻:茶與咖啡) (Tree-based Consistency Objective Function For alignment Evaluation) (以樹形基礎的一致性做多重序列比對) 是利用漸進似演算法來作多重序列比對的軟體。 它利用兩兩序列比對所產生的資訊來進行多重序列比對。 在最新的版本 (3D-Coffee) 中，亦可結合結構的資訊來作多重序列比對。 此外，該軟體可以評估比對結果的品質及找出在比對中所出現特殊的模板 (Mocca)。 預設比對結果輸出的格式為 aln (Clustal), 但也可產生其他 PIR, MSF, FASTA ... 等格式。 常用的輸入格式多有支援 (FASTA, PIR)。

子方法

M-Coffee

M-Coffee 是 T-Coffee 中一個特別的方法，它可以結合許多常用的多重序列比對的軟體，例如：Muscle, ClustalW, Mafft, ProbCons ... 等。 所產生出來的結果將比個別方法來的好一些，然而更重要的一點是在 M-Coffee 將指出比對結果中各方法所同意的區段出來，各方法所同意的區段通常是可靠的比對結果。

Link

Linux/Unix users

1. download the installer package available here (or the latest beta here);
2. open a terminal window, move to the download path, and grant execute permission to the installer typing the following command:
   chmod +x T-COFFEE_installer_Version_9.03.r1318.bin
3. launch the installer
   ./T-COFFEE_installer_Version_9.03.r1318.bin
4. when the installation procedure has finisched open a new terminal window (so that changes made by the installer are effective) and type the following command to verify your installation:
   t_coffee -version

Error: >> t_coffee: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by t_coffee)

Code:

find / -name /lib/libc.so*

This will give some files like /lib/libc.so.4 or /lib/libc.so.5 or some number at the end.

Then, just make a soft link.

Code:

ln -s /lib/libc.so.4  /lib/libc.so.6.

This has worked for me several times, should work for you too.


Command line

 t_coffee ZF.txt -output aln, score_html -mode mcoffee