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Computational Tools |
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github.com/David-Peede/RIPTA RIPTA: Package to calculate site pattern based summary statistics described in Peede et al. 202X. |
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github.com/Jazpy/adnator aDNAtor: blazing fast read simulation for related individuals. Includes simulation of parameters such as demographic history, deamination, coverage, contamination, and genotyping error. An alternative to github.com/Jazpy/adnatorgargammel or NGSNGS if you're looking to simulate many samples at once. |
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Haplostrips: Haplostrips produces plots that depict variants in a genomic window among different samples. Visualize similarities between haplotypes with respect to a reference haplotype through haplotype clustering and sorting, useful for revealing hidden population structure. The figure displays the haplotypes in the LCT gene. |
