sample-control-file.ctl

GENERAL-INFO-START

	seq-file            seqs-sample.txt
	trace-file          out/sample-trace.tsv
    comb-stats-file     out/sample-comb-trace.tsv
    clade-stats-file    out/sample-clade-trace.tsv
    hyp-stats-file      out/sample-hyp-trace.tsv

	locus-mut-rate      CONST


	mcmc-iterations     5000
	mcmc-sample-skip    4
	iterations-per-log  50
	logs-per-line       10


	find-finetunes		FALSE
	finetune-coal-time	0.01		
	finetune-mig-time	0.3		
	finetune-theta		0.04
	finetune-mig-rate	0.02
	finetune-tau		0.0000008
	finetune-mixing		0.003
#   finetune-locus-rate 0.3
	
	tau-theta-print		10000.0
	tau-theta-alpha		1.0			# for STD/mean ratio of 100%
	tau-theta-beta		10000.0		# for mean of 1e-4

	mig-rate-print		0.001
	mig-rate-alpha		0.002
	mig-rate-beta		0.00001

GENERAL-INFO-END

CURRENT-POPS-START	

	POP-START
		name		A
		samples		one d
	POP-END

	POP-START
		name		B
		samples		two d
	POP-END

	POP-START
		name		C
		samples		three d
	POP-END

	POP-START
		name		D
		samples		five d
	POP-END
	
CURRENT-POPS-END

ANCESTRAL-POPS-START

	POP-START
		name			AB
		children		A		B
		tau-initial     0.000005
		tau-beta		20000.0	
		finetune-tau	0.0000008
	POP-END

	POP-START
		name			ABC
		children		AB		C
		tau-initial     0.00001
		tau-beta		20000.0	
		finetune-tau	0.0000008
	POP-END

	POP-START
		name			root
		children		ABC	D
		tau-initial     0.00005
		tau-beta		20000.0	
		finetune-tau	0.00000286
	POP-END

ANCESTRAL-POPS-END

MIG-BANDS-START	
	BAND-START		
       source  D
       target  B
       mig-rate-print 0.1
	BAND-END
MIG-BANDS-END