Cialign

Changelog:
* Changed how the main CIAlign.py script works internally (but not the results) by moving the argument parser to argP.py and the code to run CIAlign from CIAlign.py to runCIAlign.py and split it up into functions, added extra comments and docstrings
* Added an option to the miniAlignments to keep the numbering from the initial alignment in the mini alignment for the output (e.g. if the input is 1, 2, 3, 4 and 3 is removed the rows in the output will be numbered 1, 2, 4 rather than 1, 2, 3.
* Added default, minimum and maximum values to all the numeric parameters
* Added two additional amino acids - U and O - to the mini alignment colour dictionary
* Added an option to parse non-CIAlign log files to the benchmarking AlignmentStats find_removed_cialign function
* Added --clean, --interpret, --visualise options to run multiple functions
* Added --logo_start, --logo_end to make a sequence logo for partial sequences
* Additional scripts to show how benchmarking was performed
* Generated online figures and online tables for manuscript
* Minor fixes to unit tests to accomodate changes in the main code
* Minor bug fixes and additional documentation

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