Testing files for comparing statistics between ms output and scrm ouput

CHECKING THE INITIAL TREE
	
* Checking -T option
(Good 19Jan14) ##############################################
(GOOD 17 May 14)
(GOOD 1 June 14)
	Compare TMRCA
		./ms_vs_scrm-tmrca.sh
	
	Output file:
		test-tmrca/compareTMRCA
		test-tmrca/*.pdf
		
(Good 19Jan14) ##############################################
(GOOD 17 May 14)
(GOOD 1 June 14)
	Compare total branch length
		./ms_vs_scrm-bl.sh
	
	Output file:
		test-bl/compareBL
		test-bl/*.pdf


(Good 19Jan14) ##############################################
(GOOD 17 May 14)
(GOOD 1 June 14)
	Compare number of segregating sites (mutations)
	./ms_vs_scrm-seg.sh 
	
	Output file:
		test-seg/compareSEG
		test-seg/*.pdf

* Checking segregating sites data
(Good 27Jan14) ##############################################
(GOOD 17 May 14)
(GOOD 31 May 14)

	Compare summary statistics of the segregating site statistics (see ms manual section: Using ms with sample_stats)
	./ms_vs_scrm_SEG_samplestats.sh
	
	Output file:
		test-SEGsamplestats/compareSEG
		test-SEGsamplestats/*.pdf

CHECK TMRCA TOTAL BL SEG IN THE FOLLOWING CASES

* Checking -ma option	
(Good 28Jan14) ##############################################
(GOOD 17 May 14)
(GOOD 31 May 14)

	Compare TMRCA and total branch length, and segregating sites for migration
	./ms_vs_scrm-mig.sh
	
	Output file:
		test-mig/compareMIG  
		test-mig/*.pdf
        
(Good 27Feb 14) ##############################################
(GOOD 17 May 14)
(GOOD 31 May 14)

	Compare TMRCA and total branch length, and segregating sites for migration BETWEEN TWO SEQUENCES
	./ms_vs_scrm-mig_more.sh
	
	Output file:
		test-mig-more/compareMIG  
		test-mig-more/*.pdf
        
			
* Checking the population structure, -eN option
(Good 19Jan14) ##############################################
(GOOD 17 May 14)
(GOOD 31 May 14)
	Compare TMRCA and total branch length, and segregating sites for Population structure
	./ms_vs_scrm_pop_struct.sh 

	Output file:
		test-POP/comparePop
		test-POP/*.pdf

NOTE: Tajima's D only works when sample at least 3 individuals. Therefore, case 1 and 2 in the experiment would not work as the sample sizes are only 2

* Checking -ma option with -eN option
(Good 28Jan14) ##############################################
(GOOD 17 May 14)
(GOOD 31 May 14)
	Compare TMRCA and total branch length, and segregating sites for migration
	./ms_vs_scrm-mig-popsize.sh 
	
	Output file:
		test-mig-popsize/compareMIG  
		test-mig-popsize/*.pdf

* Checking the sub population structure, -en, and -ej options
(GOOD 13Feb14)##############################################
(GOOD 17 May 14)
(GOOD 31 May 14)

	Compare TMRCA and total branch length, and segregating sites for migration
    ./ms_vs_scrm_subpop_struct.sh
    
    Output file:
        test-SUBPOP/compareSubPop
        test-SUBPOP/*pdf

* Checking growth rate, -G, -eG, and -eg option
(GOOD 10APR14)##############################################
(GOOD 17 May 14)
(GOOD 31 May 14)

    Compare TMRCA and total branch length, and segregating sites for migration
    ./ms_vs_scrm_growth.sh 
    
    Output file:
        test-GROWTH/compareGrowth
        test-GROWTH/*pdf


WITH RECOMBINATION
	
(Good 27Jan14)	##############################################
(retest 17 May 14)
(GOOD 1 June 14)
	Compare TMRCA
	Compare total branch length

	./ms_vs_scrm-tmrca-wit-recomb.sh
	
	Output file:
        test-tmrca-recomb/compareTMRCA-RECOMB
        test-tmrca-recomb/compareBL-RECOMB
        test-tmrca-recomb/*pdf
	
	
(Good Feb 10)	##############################################
(GOOD 1 June 14)
	Compare number of segregating sites (mutations)
	./ms_vs_scrm-seg_wit_recomb.sh 
    
    Output file:
        test-seg-recomb/compareSEG-RECOMB 
        test-seg-recomb/*pdf

NOTE: for most of the cases, there is no significant difference on number of segreating sites. However, if there are only two lineages. The frequncy of few mutations differ.    


* Checking -ma option with -r option
(Good 27Feb14) ##############################################
(GOOD 17 May 14)
(GOOD 31 May 14)
	Compare TMRCA and total branch length, and segregating sites for migration
	./ms_vs_scrm-mig_recomb.sh
	
	Output file:
		test-mig-recomb/compareMIG  
		test-mig-recomb/*.pdf
        
(Good 27Feb14) ##############################################
(GOOD 31 May 14)

	Compare TMRCA and total branch length, and segregating sites for migration BETWEEN TWO SEQUENCES
	./ms_vs_scrm-mig_more_recomb.sh
	
	Output file:
		test-mig-pair/compareMIG  
		test-mig-pair/*.pdf
        

        
	##############################################
	Compare spectrum
	Compare the Spectrum of the segregating sites, frequencies of observing a k mutation...
 (In process 18Jan14, need to check 19Jan14)   
    ./spectrum.sh

    ./spectrum-wit-recomb.sh
    
    Output file:
        test-spectrum/compareSPEC

test-spectrum-recomb/    


* Checking growth rate with recombination, -G, -eG, and -eg option
(GOOD 1 June 14)##############################################
    Compare TMRCA and total branch length, and segregating sites for migration
    ./ms_vs_scrm_growth-recomb.sh 
    
    Output file:
        test-GROWTH-recomb/compareGrowth
        test-GROWTH-recomb/*pdf
	
	
RECOMBINATION ONLY
	
(GOOD 18Jan14)	##############################################
	Compare number of recombination
	./ms_vs_scrm-recomb.sh
	
    Output file:
        test-recomb/compareRECOMB
        test-recomb/*pdf
	
	
	##############################################
	Compare LD
	
	##############################################
	Pairwise differences, see Excoffier and Foll 2011, Supplementary information. 
!!! Need to test for the two island model
	./pairwise_test.sh
	
	
	
	


