Using the function drop.tip() from the R package ape, this tool trims a selected subset of bee species from trees containing up to 4,586 species.
Instructions
Choose taxonomic rank (family or subfamily), and choose from the lists to display species in the left window.
Select species to copy them into your list in the right window. You can continue to select from multiple taxonomic ranks after copying species into your list. You may also copy and paste directly into the list window from our full species list. See our taxonomic database for details about the nomenclature used.
Select “Get trees” to download a zipped set of 1000 trees.
If you wish to add taxa to the phylogeny, there are multiple tools that have been made available in recent years for this purpose. Examples of some of these tools are the R packages ‘PASTIS’ (Thomas et al., 2013), ‘regPhylo’ (Eme et al., 2019) and ‘U.PhyloMaker’ (Jin and Qian, 2022), the ‘PUmPER’ framework written in Ruby programming language (Izquierdo-Carrasco et al., 2014), the tools ‘PyPHLAWD’ (Smith and Walker, 2019) and ‘SuperCRUNCH’ (Portik and Wiens, 2020) written in Phyton programming language, and the Python packages ‘OpenTree’ (McTavish et al., 2021) and ‘Physcraper’ (Sánchez-Reyes et al., 2021).
References
- Eme, D., Anderson, M.J., Struthers, C.D., Roberts, C.D., Liggins, L., 2019. An integrated pathway for building regional phylogenies for ecological studies. Global Ecology and Biogeography, 28(12), 1899–1911. doi:10.1111/geb.12986.
- Izquierdo-Carrasco, F., Cazes, J., Smith, S.A., Stamatakis, A., 2014. PUmPER: Phylogenies updated perpetually. Bioinformatics, 30(10), 1476–1477. doi:10.1093/bioinformatics/btu053.
- Jin, Y., Qian, H., 2022. U.PhyloMaker: An R package that can generate large phylogenetic trees for plants and animals. Plant Diversity, 45(3), 347-352. doi:10.1016/j.pld.2022.12.007.
- McTavish, E.J., Sánchez-Reyes, L.L., Holder, M.T., 2021. OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life. Systematic Biology, 70(6), 1295–1301. doi:10.1093/sysbio/syab033.
- Portik, D.M., Wiens, J.J., 2020. SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets. Methods in Ecology and Evolution, 11(6), 763–772. doi:10.1111/2041-210X.13392.
- Sánchez-Reyes, L.L., Kandziora, M., McTavish, E.J., 2021. Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life. BMC Bioinformatics, 22(1), 355. doi:10.1186/s12859-021-04274-6.
- Smith, S.A., Walker, J.F., 2019. PyPHLAWD: A python tool for phylogenetic dataset construction. Methods in Ecology and Evolution, 10(1), 104–108. doi:10.1111/2041-210X.13096.
- Thomas, G.H., Hartmann, K., Jetz, W., Joy, J.B., Mimoto, A., Mooers, A.O., 2013. PASTIS: An R package to facilitate phylogenetic assembly with soft taxonomic inferences. Methods in Ecology and Evolution, 4(11), 1011–1017. doi:10.1111/2041-210X.12117.
