Cialign

Changelog
Added unit tests
Added benchmarking scripts
Changed default parameters for remove_insertions and remove_divergent
Minor bug fixes

Changlog

Changelog:

* Resolved issue with pip install
* Added small additional functionality to makeSimilarityMatrix function to count positions with one gap and one non-gap
* Allowed for ambiguous amino acid codes
* Added checks that files are valid FASTA files and that all residues are recognised
* Minor debugging

Changelog
* Updated miniAlignments to work with large alignments in the latest version of matplotlib
* Small performance improvements to remove_insertions
* Changed the _removed.txt log file to allow automated processing
* Improved log file to remove unnecessary logging
* Changed minimum number of sequences in an alignment to two where this is appropriate
* Formatting to match pep8 standard
* Improved error messages
* Minor bug fixes

Improved error handling
Modifications to manual
Additional crop_ends parameter
Minor debugging

Latest release