uMUSCLE plugin: A visual interface for MUSCLE package

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uMUSCLE and uMUSCLE4 plugins

UGENE contains graphical ports of two Robert C. Edgar's tools for multiple alignment: MUSCLE and MUSCLE 4.

This packages are integrated completely, so there is no need in extra files for using these tools. Plugins allow you to run several multiple alignment tasks in parallel, check the progress and cancel running tasks safely.

To run classic MUSCLE use the "Align->Align with MUSCLE" context menu of multiple alignment editor.

MUSCLE 4 is not configurable yet and uses only default settings.

The dialog contains list of predefined MUSCLE configurations, like "Default", "Large alignment", "Refine only" etc. These presets are identical to the described ones from original MUSCLE user guide

Note, that by default UGENE does not rearrange sequence order in alignment, but the original MUSCLE package does. To enable sequence rearrangement use "Do not rearrange sequences" check button.

One of the improvements to the original MUSCLE package is the ability to align only a part of the model. When 'Custom range' mode is used only a region of specified columns is passed to the MUSCLE alignment engine. The resulted alignment is inserted into the original one with gaps added or removed on region boundaries.

The menu "Align->Align profile to profile with MUSCLE" allows to align an existing profile to the active alignment. During this process MUSCLE does not realign the profiles, but inserts columns with gaps characters only ('-' characters). For example, the alignment in the picture below could be used as a profile:

The same profile after profile-to-profile alignment:

There are two gap columns inserted into the source profile, and two gap columns inserted into the added one. Therefore the profiles columns kept intact and the alignments haven't been changed.

Note, that aligning a profile to the active alignment you will modify the original alignment file, since it will contain 2 profiles after the operation is completed.

Another feature provided by the plugin is aligning set of unaligned sequences to the existing profile. To use this feature select "Align->Align sequences to profile with MUSCLE" menu.

This option is not available in the original MUSCLE package (v3.7) and is a new functionality for original MUSCLE users. In this mode every sequence from 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 aligment 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 modified.

Note, that if a file with another alignment is used as a source of unaligned sequences, the gap characters are removed and every 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 less about 5 minutes on the usual Core2Duo computer.

Integrated optimizations:

The k-mer clustering part of the MUSCLE algorithm was optimized for multicore systems by Timur Tleukenov, Novosibirsk State Technical University