Using ClustalX for multiple quence alignment
足球颠球技巧
Jarno Tuimala
池州市人力资源和社会保障局December 2004
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Index
Index (3)
Quick Start (4)
列式1. Open ClustalX (4)
2. Read in the FastA-formatted quences (4)
3. Modify the output format option, if necessary (5)壁纸大全图片
4. Create an alignment (5)
Creating the input file for multiple quence alignment (6)
Multiple alignment theory (7)
Getting the data into ClustalX (8)
Setting up the alignment parameters (9)
Pairwi alignment parameters (9)
玄关什么意思Multiple alignment parameters (11)desktop是什么
Alignment output-format (12)
Creating the alignment (13)
Writing alignment as Postscript (14)
Asssing the quality of the alignment (15)
Advanced alignment strategies (16)
Advanced options (17)
Do alignment from the guide tree (17)
Profile alignment (17)
Using condary structure information in the profile alignment (19)
Quick Start
In order to make a multiple quence alignment using ClustalX, you should have your quences in FastA format. If you do not know haw to do this, check the chapter “Creating the input file for multiple quence alignment”.
1. Open ClustalX
After starting ClustalX, and you will e a window that looks something like the one below.职业类的英语单词
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2. Read in the FastA-formatted quences
Pull down the File-menu, and choo Load Sequences menu item. Navigate to the folder (subdirectory) that contains the input file (text-file containing the quences in FastA-format), and choo that file. Sequences should appear in the ClustalX window.
The left pane (in the figure above) lists the quences according to the name that follows “>” symbol in the input file. The right pane shows the beginning of each quence. You can scroll to the right to e the rest of each quence by using the scroll bar at the bottom of the pane.
3. Modify the output format option, if necessary
Before aligning the quences, you should make sure the output format options (from menu Alignment -> output format options) are t correctly. If you’d like to continue with phylogenetic analysis using Phylip package, you should lect PHYLIP format. Note, that you should always save the Clustal formatted quence alignment, also. Here’s an example of the output format option ttings:
4. Create an alignment
In order to make the actual alignment, lect “Do complete alignment” from the menu Alignment. At that point ClustalX asks for output file names. Your quence alignment is automatically saved in tho files once the alignment is ready. After the alignment has been successfully calculated, a new view will appear, and it might look something like that:
Now that the alignment has been created, you can clo ClustalX, and u the generated alignment files in other programs.
