Have you compared the output of PACo to other methods like Parafit?

It's great that you've deposited your sequences in GenBank. Could you provide the GenBank accession numbers of all sequences used in this manuscript? Again, it would help to know the identity of the data analysed in this article.

Could you please provide the alignment data & the phylogenetic tree(s). Without this the article is less useful to me & perhaps others.

Some advice on the why's & how's is given in this recent article: http://currents.plos.org/treeoflife/article/best-practices-for-data-sharing-in-phylogenetic-research/

figshare, zenodo, Dryad, TreeBASE, or supp data with PeerJ, any of these would suffice as...