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1. flu-crew/Fluminaflu-crew/FluminaPublic

   A pipeline for the analysis of Illumina sequence data from Influenza viruses

   R 4 2

2. FrogCap-Sequence-CaptureFrogCap-Sequence-CapturePublic

   Probe set files and pipeline for the analysis of data acquired from the Hutter et al. (2021) sequence capture probe set for all frogs

   R 9 1

3. PhyloProcessRPhyloProcessRPublic

   R package for processing high-throughput sequencing data from targeted sequence capture for phylogenomic analyses

   R 3

4. MitoTrawlRMitoTrawlRPublic

   An R package for processing high-throughput sequence data from raw reads to alignments from mitochondrial genomes sequenced as by-catch

   R 1 1

5. PhyloConfigRPhyloConfigRPublic

   Configures various phylogenetic software input and output parsing

   R 2

6. flu-crew/dairy-cattle-hpai-2024flu-crew/dairy-cattle-hpai-2024Public

   code to reproduce analysis in Nguyen et al.

   R 3