Are interphylum spiralian relationships resolvable?

While the membership of the major animal clade of Spiralia has been relatively stable since the introduction of molecular sequence data, the relationships between the constituent phyla are less clear. Focusing on the five largest phyla (Annelida, Brachiopoda, Mollusca, Nemertea, and Platyhelminthes), we find previous analyses have supported all 15 possible unrooted trees that could relate them, suggesting a hard-to-resolve node. We have used two recent phylogenomic data sets to explore this remarkable example of taxonomic instability. Using a combination of taxon-jackknifing and bootstrapping on empirical and simulated data, we explored the support for all 105 rooted and 15 unrooted 5-phylum topologies under site-homogeneous and site-heterogeneous substitution models. Rooted analyses suggested that the preference for rooting Spiralia on Platyhelminthes is due to artefactual long-branch attraction between this clade and Gnathifera. Most unrooted analyses showed a marginal and non-signifi..., , # Are interphylum spiralian relationships resolvable?

## Directory list:

For all folders:

* MARL subfolders contain the data from and analyses based on [Marlétaz et al. 2019](https://doi.org/10.1016/j.cub.2018.11.042)
* SERR subfolders contain the data from and analyses based on [Serra Silva et al. 2025](https://doi.org/10.1016/j.cub.2025.06.045).
* Any files with 'Pasc' in the name belong to this data set.

For all folders, except `results.zip`, the order of the 105 rooted topologies does not correspond to that depicted in [Serra Silva and Telford 202x](TBA).
To covert between raw analyses and plots use this re-ordering: (99:105,8:14,15:21,1:7,22:28,29:35,36:42,43:49,50:56,57:63,64:70,71:77,78:84,85:91,92:98)

`Alignments.zip` folder: contains the concatenated alignments used for fixed-taxon topology-scoring analyses

* Concatenated:
* MARL:
* Marl_clanChecked_LophOgps_concat_70k.fasta: concatenated matrix for 105-rooted topology analyses
* Marl_clanChecked_LophOgps_conc..., ,