Sequence Realignment

Choosing Edit... Realign Sequences from the Multalign Viewer menu opens a dialog for generating a new multiple sequence alignment (MSA) from all of the sequences in the current alignment. The current alignment is not used; the sequences are submitted in a dealigned state to a Clustal Omega or MUSCLE web service provided by the UCSF RBVI. The MSA web service is also used by Align Chain Sequences to align the sequences of structure chains in Chimera. See also: alignment editing, Match -> Align

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG. Mol Syst Biol. 2011 Oct 11;7:539.

MUSCLE: multiple sequence alignment with high accuracy and high throughput. Edgar RC. Nucleic Acids Res. 2004 Mar 19;32(5):1792-7.

Options (default settings bold):

• Open realigned sequences in (the current alignment window/a new alignment window) - whether to replace the existing alignment or to open the new alignment in an additional Multalign Viewer window (default); if the latter:
  • Title for new alignment window (default Realigned Sequences) - text for the title bar of the new Multalign Viewer window and the corresponding instance in the Tools menu
  
  
• Alignment program (Clustal Omega/MUSCLE) - whether to use Clustal Omega (default) or MUSCLE

  If Clustal Omega [see the README file at the Clustal Omega website for details]:

  • Number of guide-tree/HMM iterations (1) - how many combined guide tree/HMM iterations to perform after the initial alignment; can be 0 [--iterations]
  • Use full distance matrix during initial alignment (true/false) - whether to use the full distance matrix for guide-tree calculation during the initial alignment [--full]
  • Use full distance matrix during alignment iteration (true/false) - whether to use the full distance matrix for guide-tree calculation during iteration, if any [--full-iter]

  If MUSCLE [see the command-line reference at the MUSCLE website and BMC Bioinformatics 5:113 (2004) for details]:

  • Maximum number of iterations (16) - maximum number of iterations [-maxiters]
  • Maximum time to iterate in hours (0 means no limit) (0.0) - maximum run time [-maxhours]
  • Find diagonals (faster execution if sequences are similar) (true/false) - whether to use segments of high sequence similarity to constrain the alignment; may improve speed but at the expense of some accuracy [-diags]

OK initiates the calculation and dismisses the dialog, whereas Apply initiates the calculation without dismissing the dialog. The job will be run in the background; clicking the information icon in the Chimera status line will bring up the Task Panel, in which the job can be canceled if desired. Close dismisses the dialog, and Help opens this manual page in a browser window.