SuiteMSA :
Visual Tools for Multiple Sequence Alignment Comparison and Molecular Sequence Simulation
What is SuiteMSA :
SuiteMSA is a java-based application that provides unique MSA viewers. Users can directly compare multiple MSAs and evaluate where the MSAs agree (are consistent) or disagree (are inconsistent). SuiteMSA also provides a GUI for a sequence evolution simulator (iSGv2) as well as a graphical phylogeny editor/viewer.
Downloads:
    SuiteMSA package (v1.3.22B)[zip file]
    SuiteMSA (v1.3.22B)[dmg file](for MacOS X)
    Free source license
    Start using SuiteMSA instructions
    SuiteMSA_1.2 User Manual (6-14-11)
    SuiteMSA_1.3 Addendum(available 5-22-12)
    Compatible iSGv2.1.06 [tar.gz file]
    Compatible iSGv2.1.06 [zip file]
Six main tools:
  • MSA Viewer: a single MSA viewer with insertion/deletion tracking and secondary strucutre and transmembrane prediction displays   New features
  • MSA Comparator: pairwise MSA comparison, including sum of pair scores and columne scores  New features
  • Pixel Plot: multiple MSA comparison using pixel plots  New features
  • iSG Simulation: sequence simulation by iSGv2
  • Phylogeny Viewer: a graphic phylogeny viewer/editor
  • MSA reconstruction GUI's: Muscle and ClustalW2 alignment
Other package links:
    indel-seq-gen website:    iSG
    SATé primary website:    SATé
    Muscle primary website:    Muscle
    MAFFT primary website:    Mafft
    ClustalW2 primary website:    ClustalW2
Contacts:
contact image
  Version 1.3
Development of SuiteMSA has been supported by NSF AToL grant 0732863.
Whats New?
Mac OS, Linux, and MSwindows compatable
Tutorial Data:
Handout and data for SuiteMSA workshop
Publications:
Catherine L. Anderson, Cory L. Strope, Etsuko N. Moriyama (2011) SuiteMSA: Visual Tools for Multiple Sequence Alignment Comparison and Molecular Sequence Simulation. BMC Bioinformatics 12:184.
Catherine L. Anderson, Cory L. Strope, Etsuko N. Moriyama (2011) Assessing Multiple Sequence Alignments Using Visual Tools. Bioinformatics - Trends and Methodologies (ed. Mahdavi, M. A.) InTech (ISBN 978-953-307-282-1)
Supplemental files
What's New
02/17/2013     (v1.3.22B)
Bugs addressed:
  • Ranked data color corrected
  • edited file can be saved
  • display issues corrected
Coming soon
  • GUI for Mafft alignment program
  • Addendum for new feature in V1.3 posted

 
02/16/2013     (v1.3.21B)
Bugs addressed:
  • Additional display issue regulated
Coming soon
  • GUI for Mafft alignment program
  • Addendum for new feature in V1.3 posted

 
01/12/2013     (v1.3.20B)
New features:
  • Windows friendly MSAviewer, MSA Comparator, and pixel plot
Bugs addressed:
  • Display issue regulated
Coming soon
  • GUI for Mafft alignment program
  • Addendum for new feature in V1.3 posted

 
05/31/2012     (v1.3.15B)
New features:
  • Cline Shift Score and columnwise display added to MSA Comparator
Bugs addressed:
  • MSA Comparator Display corrected to display data in appropriate locations
Coming soon
  • GUI for Mafft alignment program
  • Addendum for new feature in V1.3 posted

 
05/22/2012     (v1.3.14B)
Convenience features:
  • Last directory remembered between file selections.
  • Key board short cuts added for highlight positioning
Coming soon
  • GUI for Mafft alignment program
  • Addendum for new feature in V1.3 posted

 
05/21/2012     (v1.3.13B)
New features For Pixel Plot
  • Image file generation for very large "undisplayable" pixel plot
Coming soon
  • GUI for Mafft alignment program
  • Addendum for new feature in V1.3 posted

 
05/15/2012     (v1.3.12B)
New features For MSA Viewer
  • Alignment Editing mode
  • Addition structure dinformation display
  • Color schemes based on structure information
  • Image file generation tool
  • Reverse sequence utility
New features For MSA Comparator
  • Color coded consistency measure
  • Adjustable column score threshold
  • SPS display moadified to show both acheived SPS and maximum possible SPS
  • Image file generation
  • Column score with column indication
New features For Pixel Plot
  • Structure information color schemes available
  • Image file generation
Coming soon
  • GUI for Mafft alignment program
  • Addendum for new feature in V1.3 posted

 
06/13/2011     (v1.2.06)
Changes
  • Display for TM structure characters adjusted to allow lower case characters
  • Rearrangment of Muscle and ClustalW GUIs
Users Manual for version 1.2 (06) posted
06/11/2011     (v1.2.05)
Bug corrected
  • Sync' of TM display and alignment in MSA Viewer restored.
05/19/2011     (v1.2.01)
New features For MSA Viewer
  • Column-wise information content histogram
  • Secondary structure and transmembrane prediction display
  • Alignment statistics
  • Sequence subset extraction utility
  • Alignment sort utility
  • Choice of color schemes
  • Average hydrophobicity graph added for hydrophobicity color scheme
New features For MSA Comparator
  • Column-wise information content histogram
  • Sum of pair score for comparison
  • Column score with column indication
New features For Pixel Plot
  • Limit on number of pixel plots removed
New feature
  • GUI for muscle alignment program
01/15/2011     (v1.1)
Beta Release