We need a comprehensive phylogeny that includes all of the seagrasses. All of the seagrass lineages are within the Order Alismatales. The best available Alismatales phylogeny only resolves lineages to genus, and uses a combination of morphological characters and rbcL. So, here’s what I did to produce a phylogeny of all available Alismatales with rbcL:
1. Search the NCBI Nucleotide database for “rbcl” and “partial cds”
2. Use the Taxonomic Groups filter (box on the right side of the results page) to get only the Alismatales
3. Export (Send to > file > FASTA) the 1649 Alismatales sequences in fasta format
4. Fix the sequence identifiers.
5. Align those sequences with Muscle.
6. Build tree with FastTree.
Then, I had to do a lot of manual editing to 1) highlight the seagrass species, 2) remove some matK sequences that made their way in there somehow, 3) de-replicate redundant species (when they formed monophyletic groups), and 4) reduce the tree to the smallest monophyletic clade that contained all of the seagrasses.
I would not use this tree in an analysis or publication, but for our current needs, I think this will be sufficient. Producing a high-quality, comprehensive phylogeny of the monophyletic clade that contains all seagrasses is going to be a big job.