The ReptileEvolution.com Project

Taxon exclusion is the number one problem currently vexing paleontology. The search for pterosaur, turtle, bat, snake, whale, reptile and tetrapod ancestors continues to unnecessarily befuddle traditional paleontologists who continue to work from cherry-picked, textbook and traditional taxon lists that overlook and omit pertinent taxa.
By contrast, the large reptile tree (LRT, 2340 taxa) and large pterosaur tree (LPT, 268 taxa) minimize taxon exclusion by simply having a large number of taxa. These largely resolved cladograms are at the heart of www.ReptileEvolution.com. Larger taxon numbers minimize taxon exclusion. Results resolve most former and traditional phylogenetic issues, including the nesting of former enigma taxa and clades. Some workers have suggested that more characters are the answer, perhaps not realizing that omitted taxa have no chance of affecting results. The LRT provides that opportunity. On the other hand, inappropriately included taxa in smaller studies find a more parsimonious nesting site when given the opportunity to do so.
Work continues as new taxa are added. Red taxa in PDF files have been tested then removed from the matrix due to their 'wild card' affect on other nodes, often due to incomplete or far from complete data (e.g. taxa known from only a dentary with or without teeth).
The synapsid mammal file = archo-sans-diaps has been the most difficult clade to resolve due to convergence, gender differences in the skull (crests, canines, etc), tooth count during ontogeny and available data. There is also the issue of the' double-rooted upper canine', which is shown to be a large premolar 1 in homology. Primitive taxa in two lineages (unofficially Akynodonta 1 and 2) retain a vestigial canine at the anterior edge of the maxilla. Later members reduce the double root to a single rooted canine-like premolar making identification a phylogenetic issue (= seeking a homolog), not an observational one (= following a definition). These issues may be the reason why paleontologists have turned from phenomics to genomics to resolve mammal phylogeny. Unfortunately, genomics has deep time problems = genomic results do not match phenomic results due to (perhaps) the addition of genes from invading viruses over time.
The present files are well resolved, but not fully resolved. If someone can improve on any other files with their own studies and a similar taxon list, please do so, and let us all know your results.
Good luck! Keep us informed of your progress.