Project support

Nikos Tsardakas Renhuldt helped fixing an unfortunate color choice. He also fixed bugs in --dotted mode, and contributed options --only-variable and --only-variable-excluding-indels.
Karin Lagesen @karinlag and Juan Villada @juanvillada had constructive suggestions when reviewing the paper for JOSS.
@katieemalianova help chase down installation issues.
@SimonGreenhill added support for the Nexus format.
Roey Angel reported bug about alv not guessing the MSA type correctly when a DNA/RNA sequence is completely without "codons".
Michael Milton suggested the --alignment-index option.
Marina Herrera Sarrias suggested the notebook functionality.
Ed Davies fixed a bug: sorting using option -so was broken.
Artem Kushner pointed out the missing support for sub-alignments.

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