datelife

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 . 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) . 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) . A given phylogenetic tree can be dated using time of lineage divergence data as secondary calibrations (with caution, see Schenk (2016) ). To obtain and apply secondary calibrations, the package implements the congruification method described in Eastman et al. (2013) . Tree dating can be performed with different methods including BLADJ (Webb et al. (2008) ), PATHd8 (Britton et al. (2007) ), mrBayes (Huelsenbeck and Ronquist (2001) ), and treePL (Smith and O'Meara (2012) ).

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