mash - Multiple Alignment Score HTML

FEATURES

• Displays multiple sequence alignments in HTML
• HTML5 encoding (8 to 21 characters per residue)
• Handles large MSAs
• Plug-in integration with scoring methods

SCREENSHOTS

INPUT

• ClustalW - a standard format for storing multiple sequence alignments or
• FASTA - all sequences must have the same length. Dash "-" represents a gap

OUTPUT

• HTML file - contains sequences
• JSON file(s) - results for 1 or more scoring methods

REQUIREMENTS

• R version 2.12.0 or higher
• seqinr (R library)
• rjson (R library)
• Biostrings (R library)

SCORING METHODS AVAILABLE

• Gblocks official implementation Link to website
• Gblocks unofficial open source implementation
• NorMD Link to Publication
• Substitution-matrix (e.g. BLOSUM100) column highlighter

RELATED WORK

MView

http://bioweb2.pasteur.fr/docs/mview/

"""
MView is a tool for converting the results of a sequence database search
into the form of a coloured multiple alignment of hits stacked against the
query. Alternatively, an existing multiple alignment can be processed.
"""

• Can only highlight residues based on their Physico-Chemical Properties.
• Uses <FONT> HTML tags (29 characters per residue)

T-Coffee

http://www.tcoffee.org/Projects_home_page/m_coffee_home_page.html

"""T-Coffee is a multiple sequence alignment package."""

• Highlights well-conserved residues
• In T-Coffee the HTML generator is coupled with the internal data-structures used for generating the alignments
• Uses <span> HTML tags (26 characters per residue)

GUIDANCE

http://guidance.tau.ac.il/

"""guide-tree based alignment confidence"""

• Does MSA