An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes

This repository contains sequence alignments, trees, and python scripts used for the paper: <br><br>An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes<br>Within Part_1:<br>Constraint_alignments_and_domain_IDs: This dir contains the constraint trees, and the fastas necessary for the AU comparison<br>Dating: This contains all files relevant for the dating analysis<br>Expanded alignments: this contains the various concatenates for the slow vs. fast/ number of markers test (cat1 and cat4 refer to IQTREE rate categories, 1 is slow, 4 is fast)<br>Python scripts: this includes the python scripts needed to calculate AB stem, check monophyly, convert IQTREE rate files into fasta, total tree length, and the python script to write constraint trees (from a simple .tsv)<br>Result_files: this contains the .csvs with all the results used for the paper, as well as the trees from the model/marker tests<br>Annotations_tables: contains the supplementary tables, sheets and scripts for the annotations, including table S1 in 7_Unimarkers_summary<br>Part_2_main_marker_analyses contains:<br>These are the data supplements for the analyes described in the second half of the paper,referring to the 'new' marker set constructed from multiple previous marker sets.<br>Concatenations has the various concatenations and their component alignment fatsta files, and tree files associated with them<br>Marker_analysis_Supp_scripts_tables has the various python/r/bash scripts used as well as the sheets and tables of results<br>Supp_27,54,95 has the unaligned and aligned sequences after each round of 'pruning' as well as the treefiles.<br>