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Additional analyses was performed by maximum parsimony with gaps coded as a 5th character state [ 39].
To examine the effect of considering gaps as a 5th character state rather than as missing data, we therefore recoded the data to "STANDARD" characters ([ 32]; FORMAT DATATYPE = STANDARD), explicitly set the ambiguity code placeholders, and computed the mean distances (DSET DIST = MEAN).
For nucleotide sequences, indels were treated as a 5th character.
Gaps were treated as a 5th character state.
All terminal gaps in the alignment were converted to missing (i.e. as '?' characters) and gaps '-' counted as a 5th character state.
The gaps present in these matrices are relatively short (each gap is extended over only few characters); hence, treating each single gap symbol as a 5th character state (see below) is unlikely to give too much weight to gaps.
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For some authors these would be as terse as a 140-character tweet.
if only resolving that problem was as straightforward as a 140-character tweet.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com