  The algebraic properties of flattenings and subflattenings provide direct
methods for identifying edges in the true phylogeny -- and by extension the
complete tree -- using pattern counts from a sequence alignment. The relatively
small number of possible internal edges among a set of taxa (compared to the
number of binary trees) makes these methods attractive, however more could be
done to evaluate their effectiveness for inferring phylogenetic trees. This is
the case particularly for subflattenings, and our work makes progress in this
area. We introduce software for constructing and evaluating subflattenings for
splits, utilising a number of methods to make computing subflattenings more
tractable. We then present the results of simulations we have performed in
order to compare the effectiveness of subflattenings to that of flattenings in
terms of split score distributions, and susceptibility to possible biases. We
find that subflattenings perform similarly to flattenings in terms of the
distribution of split scores on the trees we examined, but may be less affected
by bias arising from both split size/balance and long branch attraction. These
insights are useful for developing effective algorithms to utilise these tools
for the purpose of inferring phylogenetic trees.
