muscle_node
node.js wrapper for MUSCLE alignment
Getting Started
Install the module with: npm install muscle_node
Usage
node muscle_node <inputfile> [insert any flags preceeded by '-' sign and seperated by a space (from flags below)]
| FLAG | FUNCTION |
|---|---|
| -diags | Find diagonals (faster for similar sequences) |
| -html | Write output in HTML format (default FASTA) |
| -msf | Write output in GCG MSF format (default FASTA) |
| -clw | Write output in CLUSTALW format (default FASTA) |
| -clwstrict | As -clw, with 'CLUSTAL W (1.81)' header |
| -quiet | Do not write progress messages to stderr |
Get MUSCLE executable
Download MUSCLE alignment executable: node ./muscle_node/getMuscle.js
Testing
For testing use the sample input: node muscle_node ./muscle_node/test_input/DNA.fasta -msf -html
Documentation
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797.
Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, (5) 113.
Contributing
All contributions are welcome.
Support
If you have any problem or suggestion please open an issue here.
License
The MIT License
Copyright (c) 2016, dohalloran
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.