PATHd8 - a program for phylogenetic dating of large trees without a molecular clock
by  Tom Britton, Cajsa Anderson, David Jacquet, Samuel Lundqvist, Kåre Bremer

Systematic Biology 56:5, pp 741 - 752 .

FILES TO DOWNLOAD
Compiled versions for the following platforms are available:
Windows XP
Mac OS X
Linux 2.4.20-31.9 (Red Hat 9), glibc 2.3.2
Unix (Sparc)

The source files and compilation instructions are found here.
A user manual is found here.
The algorithm for the program is found here.


PATHd8 INPUT:
Tree with branch lengths in Newick format
Time constraints
(optional: name of internal nodes)
   
PATHd8 OUTPUT:
PATHd8 chronogram (calibrated ultrametric tree)
Estimated ages for all nodes
Clock test results for all nodes
PATH tree (ultrametric tree without calibration)


EXAMPLES AND INSTRUCTIONS
for PATHd8 are found in the user manual.

ABOUT THE PROGRAM
PATHd8 is implemented in the C-program PATHd8 and is freely available from this website. The program works instantaneously even for very large phylogenetic trees. (The time-complexity is O(n*t), where n is the number of nodes and t is the number of time contraints.)

Input is given as a phylogenetic tree with branch lengths. An arbitrary number of age constraints can be specified, either as fixage, minage or maxage. The output contains the chronogram obtained from the PATHd8 analysis as well as a list of estimated node ages, their mean path lengths, and their estimated substitution rates. The output also contains results from the MPL analysis described in Britton et al. (2002), which can be of interest when there are no fossil datings or if the clock hypothesis is of interest (a clock test is performed at each node). 


LITERATURE REFERENCES
The program PATHd8 is based on the manuscript Estimating divergence times in large phylogenetic trees by Tom Britton, Cajsa Lisa Anderson, David Jacquet, Samuel Lundqvist and Kåre Bremer, found in Systematic Biology 56:5, pp 741 - 752 . The abstract can be found here.

The program also performs analyses with the MPL (mean-path-length) method, as described in Britton, T., B. Oxelman, A. Vinnersten, and K. Bremer. 2002. Phylogenetic dating with confidence intervals using mean path lengths. Molecular Phylogenetics and Evolution 24:58-65.
This page was last updated October 10, 2007