Phylogenetic analysis is like a paint-by-numbers kit.
You fill in each little color by following the instructions. Or you fill in each little matrix box (taxon/character) with the correct score. Only afterwards do you see the big picture. Or only afterwards does the software produce the resulting cladogram, the big picture of hypothetical relationships.
By contrast, in traditional painting
the master artist starts with a loose sketch, then arranges elements in a composition to fit a triangle, a golden rectangle, or some other substructure. The colors, tints and shadows are added in large blocks to a canvas of the right size to fit a certain wall. Finally the details (lace, highlights, eyelashes, etc. are added.
Like a paint-by-numbers canvas,
the big picture in evolution has already happened. The “instructions” or “clues” come to us in the form of preserved and exposed traits in fossils and living taxa. We don’t have all the clues, and never will, but with what we do have we fill them in until a complete picture begins to emerge, blank spaces and all.
Likewise, the large reptile tree
(LRT) and large pterosaur tree (LPT) are large gamut cladograms that will never be completed. However, as new taxa are added the details and transitions between established taxa become finer and finer blends. The big picture, or tree topology, has been pretty steady for several years and hundreds of additions.
Make sure your taxa
are all species or specimens. Those provide good data. Avoid suprageneric taxa. By combining traits from several genera you’ll muddy the canvas. The tiny features will be lacking. You’ll cherry-pick favorites and overlook obscure details that might be Important.
Science is for everyone
Not just for PhDs. If they can create a cladogram, so can you. They test published work for validity. So do I and so can you. Along the way, you will make mistakes. I do too. Others will point out mistakes. Defend your decisions where appropriate. Fix problems at every opportunity. Follow this method and your result will echo the original tree topology. Then keep adding taxa as they become available to fill in any blank spaces.
The first time an idea is proposed
it is rarely accepted. As time goes by, some hypotheses disappear. And some should disappear. Others, whether valid or not, get headlines because the PR machinery is tilted in their favor. Still others slowly grow in acceptance and are ultimately embraced because they reflect the original tree topology we’re all trying to see more clearly.
Good luck on all your endeavors.