How can I save my alignment to a file?

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How can I save my alignment to a file?

The alignment will appear on the results page along with details of scores and guide trees. The alignment can be obtained on its own by clicking on the alignment file option at the top (.aln). This file can be opened in a separate window or saved to a file.

Is there a limit on the number of sequences or the size of the file that I submit to ClustalW?

The input for ClustalW is limited to a maximum of 500 sequences or to a 10MB file (whichever is smaller). When the input file or the number of sequences is large, ClustalW can run for days and in some cases may not finish at all. If you plan to input large amounts of data/sequences, you should use the "RESULTS: email" option and "CPU MODE: multiple".

Email jobs are allowed to run for more than 24 hours and the results are kept for a week.

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Other Frequently Asked Questions

• What are the default parameters used by ClustalW?
• Is it possible to perform bootstrap analysis or to get the Bootstrap values along with the nodes of each branch of the phylogram?
• How can I get the colour version of the alignment?
• Where can I download the ClustalW software from?
• What can I do with ClustalW?
• Why does Jalview not work for me?
• How are the pairwise alignment scores generated?
• How can I see the parameter values that are used by the ClustalW program?
• How can I save my alignment to a file?
• Is there an alternative tree drawing program that can be used for large numbers of sequences?
• More...