datelife (Q159251)

Methods and workflows to get chronograms (i.e., phylogenetic trees with branch lengths proportional to time), using open, peer-reviewed, state-of-the-art scientific data on time of lineage divergence. This package constitutes the main underlying code of the DateLife web service at <https://www.datelife.org>. To obtain a single summary chronogram from a group of relevant chronograms, we implement the Super Distance Matrix (SDM) method described in Criscuolo et al. (2006) <doi:10.1080/10635150600969872>. To find the grove of chronograms with a sufficiently overlapping set of taxa for summarizing, we implement theorem 1.1. from Ané et al. (2009) <doi:10.1007/s00026-009-0017-x>. A given phylogenetic tree can be dated using time of lineage divergence data as secondary calibrations (with caution, see Schenk (2016) <doi:10.1371/journal.pone.0148228>). To obtain and apply secondary calibrations, the package implements the congruification method described in Eastman et al. (2013) <doi:10.1111/2041-210X.12051>. Tree dating can be performed with different methods including BLADJ (Webb et al. (2008) <doi:10.1093/bioinformatics/btn358>), PATHd8 (Britton et al. (2007) <doi:10.1080/10635150701613783>), mrBayes (Huelsenbeck and Ronquist (2001) <doi:10.1093/bioinformatics/17.8.754>), and treePL (Smith and O'Meara (2012) <doi:10.1093/bioinformatics/bts492>).