Test effect of partitioning on codon position for reducing noise

glstott / PMeND

Phylogeny and Metadata Network Database

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Test effect of partitioning on codon position for reducing noise #11

Closed glstott closed 2 years ago

glstott commented 2 years ago

Pulled down Houston Delta sequences until the end of the first wave, ~August 31.
This should be a good opportunity to try out the nextflow pipeline as well.

glstott commented 2 years ago

Began process using the shiny new nextflow pipeline to generate our trees. nextflow run main.nf --input /scratch/gs69042/PMeND/data/iqtree_test/ --output_dir /scratch/gs69042/PMeND/data/ --temp_out_dir /scratch/gs69042/PMeND/data --threads 16 -with-report 04122022.html -c nextflow.config

glstott commented 2 years ago

In addition, estimating SNP distances at first two and last positions for another network layer to differentiate populations.