### PARAMETER SPECIFICATIONS
# pick and choose from these commands
# include in file "in.param"
# everything after # is ignored
# commands need to be on separate lines

### GENERAL
burnin 100							# remove the first 100 trees from the analysis

### 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 
reduce tips 0.2						# takes only 20% of the tips of the tree at random
renew trunk 1						# updates trunk, working backwards from all samples within 1 year of most recent
prune to trunk						# reduces tree to just the trunk
prune to label 1					# reduces tree to just the tips with label 1
prune to tips 0MURTOQ 0BFBESB ...	# reduces tree to just the tips specified, requires tips to begin with A-Z or 0-9		
collapse labels						# drops all separate labels, every sample considered part of the same population
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						# print highest posterior / maximum likelihood tree if tagged, 
									# if not prints the last tree of in.trees		
print rule tree						# trees are printed in Mathematica compatible rule list format
									# prints to out.rules

### 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

### LOCATION STATISTICS

summary diffusion coefficient		# summarize coefficient of diffusion by comparing Euclidean distance between nodes
summary drift rate					# summarize rate of drift along branches

skyline settings 2002 2007 0.1		# split the tree starting at 2002 and ending at 2007 in steps of 0.1
skyline xmean						# compute mean of x location across slice of tree
skyline ymean						# compute mean of y location across slice of tree
skyline xdrift						# compute rate of change of x location going from time (t) back to to (t - step)

skyline settings 0 10 0.05			
skyline drift rate from tips		# compute rate of drift at a distance t back from each tip in the tree 

### 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

### PAIR STATISTICS	

pairs diversity						# find mean and variance of diveristy between each pair of tips