Change log

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Major changes to ClipKIT are summarized here.

2.4.1 The ends_only function now handles the case where nothing gets trimmed.

2.4.0 Added a new function called ends_only, which removes sites that would be trimmed for a given mode, but only at the ends of the alignment. For example, if the sites that should be trimmed include [0, 1, 2, 4, 5, 6, 14, 15, 16] for smart-gap mode and an alignment of length 16, adding the ends_only mode will result in [0, 1, 2, 14, 15, 16] being the sites that will be trimmed. Specify this argument with -eo, --ends_only.

2.3.0 Added support for Python version 3.11

2.2.3 Fixed gap character handling. The help message was incongruent with what was happening underneath the hood.

2.1.2 Incorporate codon-based trimming. When one position in a codon gets trimmed based on the mode being used, the whole codon will get trimmed from the alignment.

1.4.0 new argument for specifying if sequences are amino acids or nucleotides

1.3.0 long description of sequences, rather than identifiers, are kept in the ClipKIT output

1.1.5 carried over code base to biopython, v1.79

1.1.0: smart-gap trimming is introduced and is now the default trimming approach used in ClipKIT. smart-gap trimming is a dynamic approach to determine the appropriate gaps threshold for an alignment.