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Another feature provided by the plugin is aligning a set of unaligned sequences to an existing profile. To use this feature select the Align ‣ Align sequences to profile with MUSCLE context menu item.

This option is not available in the original MUSCLE package (v3.7) and is a new functionality for original MUSCLE users. In this mode each sequence from the input file is aligned to the active profile separately and is merged to the result alignment only after all sequences are processed. For example, the alignment in the picture above can be used as a profile again. And the added profile can be used as a set of sequences. The result of such sequences-to-profile alignment is presented on the picture below:

The original alignment is not modified, only columns with gap (‘—’) character can be inserted.

The second profile was considered as a set of sequences and therefore is modified.

Note that if a file with another alignment is used as a source of unaligned sequences, the gap characters are removed and each input sequence is processed independently.

This method is quite fast, for example an alignment of 3000 sequences (1000 bases each) to the existing profile takes about 5 minutes on the usual Core2Duo computer.

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