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Large alignments will no longer run into serialization size limits when creating Gingr files (Issue #3), thanks to the Cap'n Proto library. Older Gingr files in the Protocol Buffer format can still be read, but will not be written (and may eventually be phased out).
Exported trees will no longer have bootstrap or branch length values for the root node, which was not standard Newick and could cause crashes when loading them back in.
Exported Fasta reference files will no longer have an extra space between the ID and description in their tags.