### PARAMETER SPECIFICATIONS
# pick and choose from these commands
# include in file "in.param"
# everything after # is ignored
# commands need to be on separate lines
### TREE MANIPULATION
push times back 2007 # push dates so that the most recent sample date is 2007
push times back 2002 2007 # push dates so that the oldest sample date is 2002 and the most recent sample date is 2007
prune to trunk 1 # reduces tree to just the trunk, working backwards from all samples within 1 year of most recent
prune to label 1 # reduces tree to just the tips with label 1
trim ends 2003 2004 # reduces tree to only those branches dated between 2003 and 2004
section tree 2002 0.25 1 # reduces tree into sections, starting at 2002, leaving windows 0.25 in width
# and moving in steps of 1
time slice 2005 # reduces tree to all ancestors of lineages that exist in 2005
# used in conjunction with diversity statistics
### TREE OUTPUT # trees are printed in Mathematica compatible rule list format
# prints to out.rules
print hp tree # print highest posterior / maximum likelihood tree
### SUMMARY STATISTICS # these statistics are carried out across the entire tree
# prints to out.stats
summary tmrca # summarize TMRCA
summary length # summarize tree length
summary proportions # summarize label proportions on trunk of the genealogy
summary coal rates # summarize coalescent rates, separate rates for each label
summary mig rates # summarize migration rates, separate rates for each label pair
summary diversity # summarize diversity between each pair of tips
# if tree is tip dated should run time_slice first
summary fst # summarize diversity between labels vs diversity within labels
summary tajima d # summarize Tajima's D. This is pairwise diversity - total tree length / a1.
### SKYLINE STATISTICS # need to walk these backward to keep window consistent across samples
# prints to out.skylines
skyline settings 2002 2007 0.1 # split the tree starting at 2002 and ending at 2007 in steps of 0.1
skyline tmrca # computes the TMRCA for time slices
skyline length # computes the total length of time slices
skyline proportions # computes label proportions for trunk along time windows
skyline coal rates # computes coalescent rates for time windows
skyline mig rates # computes migration rates for time windows
skyline diversity # computes the diversity for time slices
#skyline fst # computes the FST for time slices
#skyline tajima d # computes Tajima's D for time slices
### TIP STATISTICS # these statistics are carried out on each tip
# prints to out.tips
tips time to trunk # computes the time it takes for each tip to coalesce with the genealogy trunk