A detailed description of all changes associated with the release is in the attached PDF.
CIAlign_v1.1.0_Improvements.pdf
Briefly:
The “remove insertions” function now runs much faster, particularly when the maximum insertion size is very large
A new “crop divergent” function is now available, which allows the user to isolate the most conserved region of the alignment.
CIAlign can now generate position weight, position probability and position frequency matrices.
Users can now specify, using the retain functions, sequences which they would like CIAlign not to remove.
The plot_coverage function is now the plot_stats function and will generate three plots, showing coverage, Shannon entropy and information content per column.
Users can now extract part of an alignment based on their own coordinates, using the get_section function.
An additional colour palette is now available for mini alignments and sequence logos,
It is now possible to convert T to U in alignments, as well as U to T.
The CIAlign manual is now hosted at ReadTheDocs - https://cialign.readthedocs.io/ - and is more readable and comprehensive.
Unit test coverage is now 100% across all module files (excluding import lines and logging)
What's Changed
- Retain sequences by @KatyBrown in #45
- Crop divergent by @KatyBrown in #46
- Multiple changes for release of version 1.1.0 by @KatyBrown in #47
Full Changelog: v1.0.17...v1.1.0
