ArchaicSeeker is a series of software for detecting archaic introgression sequences and reconstructing introgression history. The latest version of this series, ArchaicSeeker 2.0, has the following three notable improvements compared with the original version of this software. First, it can automatically determine the boundary of each introgressed sequence. Next, it is capable of tracing both known and unknown ancestral sources of a given introgressed sequence. Finally, it has the ability to reconstruct the introgression history with more sophisticated introgression models.
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How to QC the input data and make the model.txt. #2
Thanks your wonderful work give me a new nemethod to deal with my job.here, i have a 2 questions,when we make the input file waht's QCs need to be considerated,like the MAF ,Genotyping rate ,HWE et,? 2,How to generate the model.txt,in my idea, need the whole genome data to generate the “Newick” tree with population(group) that we used for analysis?. Thanks again,Looking forward to your reply.
For the first question, filtrations like HWE to control the quality of sequencing data can be implemented, but MAF is not recommended.
For the second question, we have provided the example model in the example data or you can refer to the protocol.
Zhang-Rui-2018
commented
2 years ago
Thanks your wonderful work give me a new nemethod to deal with my job.here, i have a 2 questions,when we make the input file waht's QCs need to be considerated,like the MAF ,Genotyping rate ,HWE et,? 2,How to generate the model.txt,in my idea, need the whole genome data to generate the “Newick” tree with population(group) that we used for analysis?. Thanks again,Looking forward to your reply.