To learn how the ABBA BABA test works, we will be writing the code from scratch to do the test.Start a new R script. This will make it easy to re-run the whole analysis using different populations. R functions for ABBA BABA analyses ...
and f4-ratio statistics for all possible quartets of populations/species (no outgroup specified) Usage: a) Dsuite Dtrios [OPTIONS] INPUT_FILE.vcf SETS.txt b) Dsuite Dquartets [OPTIONS] INPUT_FILE.vcf SETS.txt c) Dsuite Dinvestigate [OPTIONS] INPUT_FILE.vcf.gz SETS.txt test_trios.txt ...
ABBA BABA statistics The ABBABABAstatistics are used to detectandquantify an excess ofsharedderived alleles, which canbeindicative of gene flow. Given three populationsandan outgroup with the relationship (((P1, P2),P3) O), these statistics test forsharingof genetic variationbetweenP3andP2butnot w...
Experimental:DquartetsCalculateD(ABBA-BABA)and f4-ratio statisticsforall possible quartets of populations/species(no outgroup specified)Usage:a)DsuiteDtrios[OPTIONS]INPUT_FILE.vcfSETS.txtb)DsuiteDquartets[OPTIONS]INPUT_FILE.vcfSETS.txtc)DsuiteDinvestigate[OPTIONS]INPUT_FILE.vcf.gzSETS.txttest_trios.tx...
#(2)用于Dinvestigate的test_trios.txt文件。 每行三个种群/物种,以制表符按P1 P2 P3的顺序分隔: Species1 Species2 Species3 Species1 Species4 Species2 ... ... ... ### 4 Piped VCF input #本案例中没有用到 # 可以从另一个程序(例如bcftools)将基因型数据“输送”到Dsuite Dtrios或Dsuite Dqu...
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and f4-ratio statistics for all possible quartets of populations/species (no outgroup specified) Usage: a) Dsuite Dtrios [OPTIONS] INPUT_FILE.vcf SETS.txt b) Dsuite Dquartets [OPTIONS] INPUT_FILE.vcf SETS.txt c) Dsuite Dinvestigate [OPTIONS] INPUT_FILE.vcf.gz SETS.txt test_trios.txt ...