Requirements

[ebrintn]

• [ ] Obtain datasets for SARS-CoV-2, HIV-1 and the human genome
• [ ] Align sequence databases - MAFFFT?
• [ ] Theta - Watterson's, Pi, lamarc, BEAST
• [ ] Analyze results - significance between software tools

[ebrintn]

SARS-CoV-2 dataset:

• Complete (>29000 nucs) high coverage (<1%Ns and <0.05% amino acids not seen elsewhere) sequences from December 1, 2023 - January 1, 2024
• Total of 1603 sequences

continent Asia Europe North America Oceania South America 60 1068 387 69 19

[ebrintn]

HIV-1 Dataset Los-Alamos Compendium HIV-1 sequences from 2021, all subtypes 198 sequences

These sequences are already aligned by the Los Alamos research centre

[ebrintn]

Getting Watterson's theta, Lamarck and Pi

• Watterson's theta - package RPANDA (https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12526)

[ebrintn]

• [x] Watterson's
• [x] Pi
• [ ] Lamarc
• [ ] BEAST

[ebrintn]

Whole human genome sequence databases are hard to get. As a result I moved to BRCA1 genes from homo sapiens

[ebrintn]

For BRCA1 genome database: downloaded reference sequence - https://www.ncbi.nlm.nih.gov/nuccore/262359905 grabbed 100 similar sequences using blastn (not megablast because too similar)