Dataset for: An Introduction to Structural Phylogenetics for Biomedical Sciences

The datasets and scripts here accompany a pipeline for structural phylogenetics using the 3Di alphabet. The pipeline is detailed in "An Introduction to Structural Phylogenetics for Biomedical Sciences".

Directories (in order of pipeline)

query/ contains the query structure coordinate file used in the homolog search

structures/ contains the hit corodinate files from a Foldseek search

accessions/ contains the accession numbers of these hits

split/ contains the structures split into individual domains

splitfilter/ contains these splits that were confirmed to be homologous with the query

alignments/ contains the amino acid and 3Di alignments between the query and the structures in splitfilter/

trees/ contains the IQ-TREE output files

matrices/ contains 3Di substitution matrices used by IQ-TREE

figures/ contains pictures of the trees

scripts/ contains code used throughout various steps in the pipeline