datelife
CRANdatelifeMaRDI QIDQ159251FDOQ159251
Scientific Data on Time of Lineage Divergence for Your Taxa
Tracy Heath, Luna L. Sanchez Reyes, Jonathan Eastman, Klaus Schliep, Joseph Brown, Matt Pennell, April Wright, Luke Harmon, Peter Midford, Brian O'Meara, Scott Chamberlain, Mike Alfaro
Last update: 19 June 2023
Copyright license: GNU General Public License, version 3.0, GNU General Public License, version 2.0
Software version identifier: 0.6.7, 0.6.0, 0.6.1, 0.6.5, 0.6.6, 0.6.8
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>).
- SDM: A Fast Distance-Based Approach for (Super)Tree Building in Phylogenomics
- Groves of Phylogenetic Trees
- Consequences of Secondary Calibrations on Divergence Time Estimates
- Congruification: support for time scaling large phylogenetic trees
- Phylocom: software for the analysis of phylogenetic community structure and trait evolution
- Estimating Divergence Times in Large Phylogenetic Trees
- MRBAYES: Bayesian inference of phylogenetic trees
- treePL: divergence time estimation using penalized likelihood for large phylogenies
This page was built for software: datelife
