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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
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