Tutorial: Multiple Sequence Alignment with MUSCLE

Alignment with Muscle

Here we discuss the most popular topics from UGENE forum and provide you with the useful tutorials of UGENE, a free cross-platform genome analysis suite.


Let's open a file with multiple sequence alignment. As always, the file and its contents list have appeared in Objects area of current Project view, and the contents have been displayed at the multiple sequence alignment editor (or multiple alignment editor).

The topmost part of the view is Consensus area. It contains a consensus sequence in the middle, the most widespread nucleotide diagram and a nucleotide scale. Pointing mouse cursor anywhere at the nucleotide column, we can see the full nucleotide distribution for this position.

The part of the view placed below contains the sequences names, per-sequence offsets and the sequences themselves. Also at the bottom of the view we have names and sequences scrolls, a nucleotide search bar, the global cursor coordinates and the alignment lock status icon (our alignment object is not locked). If we scroll the sequences, the sequences offsets change correspondingly. However, the cursor and its coordinates remain still.


Now, let's finally align the opened sequences with multiple sequence comparison by widely known MUSCLE algorithm. To align the sequences with MUSCLE, bring up the context menu by right clicking anywhere at the alignment editor area, then select "Align", "Align with MUSCLE". In the appeared dialog box we can select alignment configuration (we'll choose the default one), set advanced algorithm options if needed and select a region to align. To start the align, click Align button. We also see remote run button which we will discuss later in the podcast.

Once alignment is finished the MSA editor contains sequences aligned with the MUSCLE plugin.

Additional Materials

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