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A solid understanding of population genetics theory is necessary and essential for correct interpretation of genomic data and patterns. Here I compiled a list of papers that I found helpful to build up the knowledge foundation for understanding the theory and analytical methods. (This list will be continuously updated.)
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PGDSpider is a very popular data conversion tool to prepare files for population genetic and phylogenetic programs. However, it did’t work anymore after I updated my mac (macOS 13.6, intel 2018). Today I finally figured installing an old Java version will do the job.
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Last week I updated my macOS system to latest Ventura 13.4 and I love it very much as I didn’t seem to find any issues in running my programs. However, today I encountered an unexpected issue: the save window keeps getting longer when I use MEGA11 to export fasta file from ab1 file (i.e. raw file from sanger sequencing). I have 54 new ab1 files to examine and this issue very quickly becomes a pain for me.
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I used to use PGDspider to convert fasta file to nexus file for phylogenetic analysis in MrBayes. However, after updating my macOS system, the java is not working anymore and thus PGDspider is not an option for me.
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In this year’s intense field season, I found something super cool that frog bones and eyes glow under my UV torchlight, and so as many lichens and fungi.