├── .DS_Store ├── .Rapp.history ├── .gitignore ├── Poster_introduction.pdf ├── PrimerMiner ├── .DS_Store ├── .Rhistory ├── DESCRIPTION ├── NAMESPACE ├── R │ ├── .DS_Store │ ├── .Rapp.history │ ├── Download_GB.R │ ├── Download_bold.R │ ├── Download_mito.R │ ├── Mito_GB2fasta.R │ ├── Vsearch.R │ ├── WriteConsensus.R │ ├── batch_config.R │ ├── batch_down.R │ ├── download_stats.R │ ├── evaluate_primer.R │ ├── merge.R │ ├── plot_alignments.R │ ├── primer_treshhold.R │ ├── primerversions.R │ └── strip_gaps.R ├── inst │ ├── .DS_Store │ ├── Position_v1.csv │ ├── Type_v1.csv │ ├── doc │ │ ├── Batchdownload.R │ │ ├── Batchdownload.Rmd │ │ ├── Batchdownload.html │ │ ├── Welcomme.R │ │ ├── Welcomme.Rmd │ │ ├── Welcomme.html │ │ ├── in_silico_evaluation.R │ │ ├── in_silico_evaluation.Rmd │ │ └── in_silico_evaluation.html │ ├── vsearch-1.10.2_linux_x86_64 │ └── vsearch-1.10.2_osx_x86_64 ├── man │ ├── .DS_Store │ ├── .Rapp.history │ ├── Clustering.Rd │ ├── Download_BOLD.Rd │ ├── Download_GB.Rd │ ├── Download_mito.Rd │ ├── Merge_fasta.Rd │ ├── Mito_GB2fasta.Rd │ ├── PrimerMiner-package.Rd │ ├── WriteConsensus.Rd │ ├── batch_config.Rd │ ├── batch_download.Rd │ ├── download_stats.Rd │ ├── evaluate_primer.Rd │ ├── plot_alignments.Rd │ ├── primer_threshold.Rd │ ├── primerversions.Rd │ └── strip_gaps.Rd └── vignettes │ ├── .DS_Store │ ├── .Rhistory │ ├── Batchdownload.Rmd │ ├── PrimerMiner_logo.png │ ├── Welcomme.Rmd │ ├── alignment_plot.png │ └── in_silico_evaluation.Rmd ├── README.md ├── Sample_Data ├── .DS_Store ├── .Rapp.history ├── 1 COI alignments (unprocessed) │ ├── .DS_Store │ ├── 1_Plecoptera_sub.fasta │ ├── 2_Trichoptera_sub.fasta │ ├── 3_Ephemeroptera_sub.fasta │ ├── 4_Coleoptera_sub.fasta │ └── 5_Bivalvia_sub.fasta ├── 2 COI alignments (processed) │ └── .DS_Store ├── package_tutorial.R ├── plot_alignments.pdf ├── primer_scoring │ ├── .DS_Store │ ├── 01_Plecoptera_subset.fasta │ ├── Position_v1.csv │ └── Type_v1.csv └── taxa_small.csv └── temp_changelog.txt /.DS_Store: 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