TreeTools

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) [doi:10.1371/journal.pone.0212942]; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) [doi:10.1093/sysbio/syab072], and of tree balance (Mir et al. 2013, Lemant et al. 2022) [doi:10.1016/j.mbs.2012.10.005], [doi:10.1093/sysbio/syac027]; artificial extinction (Asher & Smith, 2022) [doi:10.1093/sysbio/syab072]; import and export of trees from Newick, Nexus (Maddison et al. 1997) [doi:10.1093/sysbio/46.4.590], and TNT [https://www.lillo.org.ar/phylogeny/tnt/] formats; and analysis of splits and cladistic information.

Last 30 days

This package has been downloaded 1,372 times in the last 30 days. That's enough downloads to impress a room full of undergrads. A commendable achievement indeed. The following heatmap shows the distribution of downloads per day. Yesterday, it was downloaded 51 times.

The following line graph shows the downloads per day. You can hover over the graph to see the exact number of downloads per day.

Last 365 days

This package has been downloaded 17,273 times in the last 365 days. The downloads are officially high enough to crash an underfunded departmental server. Quite an accomplishment! The day with the most downloads was Feb 20, 2025 with 155 downloads.

The following line graph shows the downloads per day. You can hover over the graph to see the exact number of downloads per day.