Align Sequences with MUSCLE

This workflow performs multiple sequence alignment using the MUSCLE algorithm and saves the resulting alignment in a Stockholm document. Source data can be in any format containing sequences or alignments.

How to Use This Sample

If you haven’t used the workflow samples in UGENE before, please consult the “How to Use Sample Workflows” section of the documentation.

Workflow Sample Location

The workflow sample “Align Sequences with MUSCLE” can be found in the “Alignment” section of the Workflow Designer samples.

Workflow Image

The workflow appears as follows:

Workflow Wizard

The wizard contains 2 pages.

1. Input MSA(s): On this page, you must input multiple alignment file(s).

   

2. Align Sequences with MUSCLE: On this page, you can modify MUSCLE and output parameters.

   

   The following parameters are available:

   Parameter	Description
   Mode	Selector of preset configurations, offering you the choice to optimize accuracy, speed, or a compromise between the two. The default favors accuracy.
   Stable order	Do not rearrange aligned sequences (-stable switch of MUSCLE). Otherwise, MUSCLE rearranges sequences so that similar sequences are adjacent in the output file. This makes the alignment easier to evaluate by eye.
   Max iterations	Maximum number of iterations.
   Region to align	Whole alignment or column range, e.g., 1..100.
   Result alignment	Location of the output data file. If this attribute is set, the slot “Location” in the port will not be used.
   Document format	Document format of the output file.