Compatibility with ms output
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paula-tataru commented
Since this program is written to resemble ms, it would be useful if it would output the marginal trees the same way that ms does. In ms, the leaves of the trees are numbered starting from 1, while in msms they are numbered from 0. Maybe an options to switch between the two different type of numberings could be made?
delt0r commented
This is a bug. It should always do things the ms way.