Note: you probably want to use kameris instead.
This is a generator for Molecular Distance Maps, as seen in the following papers:
- Mapping the Space of Genomic Signatures
- An investigation into inter- and intragenomic variations of graphic genomic signatures
- Additive methods for genomic signatures
Some pre-generated Molecular Distance Maps may be seen here.
It uses FCGR and supports the following distances:
The SSIM distance may be accelerated with CUDA or OpenCL.
- Create folders named fasta, work, and output.
- Put fasta files in the fasta folder.
- Run the notebook called generation.nb. It will place distance matrices and some metadata in the output folder, and temporary files in the work folder.
- Use the notebook called analysis.nb to work with the distance matrices.
You may choose the groups for the plot by setting
taxaGroupsunder "Initialization + Settings".
You may also run the test suite in the tests folder.
The MIT License (MIT) Copyright (c) 2015 Stephen 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.