This is a program for generating starting trees consistent with fossil calibrations for divergence time estimation methods.
Node heights are drawn from a uniform distribution, conditional on node age constraints provided by calibrations.
Source code (Requires Unix, g++, automake, autoconf): 
starttree.tar.gz
starttree binary (Mac only): starttree
Instructions for using this program:
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Your tree must be fully bifurcating and rooted
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Your calibrations must be uniform distributions
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Calibrations cannot conflict with one another (e.g. a node cannot have a calibration that is older than the calibration on nodes older than it)
If you downloaded the binary, you will probably have to modify it so that it is executable. Do this (in terminal, in the same directory as the binary):
> chmod +x starttree
Execute the program and print the menu options:
> ./starttree -h
example:
$ starttree -tre tree.phy -cal calfile.txt -out output_tree.phy -n <numtaxa>
Here are the available options that you can change (default values are in []):
-hf : display example file formats **
-tre : tree file name **
-n : number of tips **
-cal : file name with internal node calibratons**
-out : file name for output tree** Execute the program and print information about the file formats:
> ./starttree -hf
File formats: Tree file (newick format) ----------------------------------------------- (((T1,T2),T3),(T4,T5)); ----------------------------------------------- Node Calibration file -U = uniform with min and max bounds ----------------------------------------------- 3 -U root 25.01 30.2 -U T1 T3 14.22 20.532 -U T4 T5 4.773 8.3 -----------------------------------------------
Primary contact: Tracy Heath
