This repository contains scripts and intermediate files for Cornales353 project.
r2t-hyb_manual.pdf details steps on the analysis pipeline.
scripts: Contains scripts used for analysis. Also contains the Angiosperms353 targets file and a list of the gene IDs. The scripts are mostly designed to create and submit multiple job submission scripts on a HPC cluster.
supercontigs: Contains multifasta files for each gene target with supercontig sequences output by HybPiper.
alignments: Contains multiple sequence alignments (MSA) from PASTA for each gene target.
ML_trees Contains maxiumum likelihood gene trees inferred using IQ-TREE.
UFboot_trees: Contains bootstrap replicate trees using the IQ-TREE UFboot feature.
astral_outputs: Contains outputs from the program ASTRAL-III.