These scripts are designed for sequence collection and alignment, data curation, and treefile manipulations in the construction and optimization of phylogenetic trees.
Cull Alignment File: To remove manually-curated taxa from a protein alignment.
Parse BLAST hits / Parse 'n Pull scripts: Input is tab-delineated BLAST output file. Allows filtering of hits (by coverage, percent identity, etc) and will pull corresponding unique hit IDs.
Rename Headers for Visualization: Renames BLAST-formatted FASTA headers to be compatible with downstream visualization scripts (e.g. Visualize in FigTree).
No Rain Delays: Removes double headers (duplicated taxon IDs for identical protein hits) from FASTA files without removing sequence data.
Tree Manips UDV: Uses ETE3 toolkit to overlay alignment/sequence features onto a tree. Allows for branch coloration by taxonomy.