BIOL4300 Project: Phylogenetics of Human Herpesvirus 6B

Scripts and data necessary to complete gene-specific analysis of Human Herpesvirus 6B (HHV-6B).

Folder organization

1. datasets/code: All scripts used (all R scripts ran in R version 4.5.1, all python scripts ran in Python 3.11.9)
2. datasets/input_data: All aligned, trimmed seqeunce data input into IQ-TREE v3.0.1 (https://iqtree.github.io/) and BEAST v2.7.7 (https://www.beast2.org/)
3. datasets/input_data: Raw data from IQ-TREE and BEAST
4. datasets/trees: Final trees visualizations (in pdf files) and tree files (.treefile from IQ-TREE and .tree from BEAST)

Steps

1. Get raw FASTA gene-specific data from Genbank (datasets/code/01.get_gene_fastas.R).
2. Get whole genome data from GenBank (datasets/code/02.get_complete_genomes.R).
3. Extract specific genes from whole genome data, add gene sequences to original gene FASTA files (datasets/code/03.extract_genes.py).
4. Get alignments by inputting gene FASTA files into MAFFT version 7 (https://mafft.cbrc.jp/alignment/software/)
5. Trim Alignments (datasets/code/05.trim.R).
6. Construct Trees:
   • Maximum Likelihood trees (IQ-TREE v3.0.1)
   • Bayesian trees (BEAST v2.7.7)
   • tree files are output to datasets/trees
7. Tree visualization (R [datasets/code/07.plot_Bayesian.R, datasets/code/07.plot_ML.R] and FigTree v1.4.4 (https://tree.bio.ed.ac.uk/software/figtree/)