mash - Multiple Alignment Score HTML
- Displays multiple sequence alignments in HTML
- HTML5 encoding (8 to 21 characters per residue)
- Handles large MSAs
- Plug-in integration with scoring methods
- ClustalW - a standard format for storing multiple sequence alignments or
- FASTA - all sequences must have the same length. Dash "-" represents a gap
- HTML file - contains sequences
- JSON file(s) - results for 1 or more scoring methods
- R version 2.12.0 or higher
- seqinr (R library)
- rjson (R library)
- Biostrings (R library)
- Gblocks official implementation Link to website
- Gblocks unofficial open source implementation
- NorMD Link to Publication
- Substitution-matrix (e.g. BLOSUM100) column highlighter
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)
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)
"""guide-tree based alignment confidence"""
- Does MSA