Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records
Amino Acid Comparison
First Modal Amino Acid Conservation
First and Second Modal Amino Acid Conservation
Amino Acid Count
Find amino acid singles
Amino Acid Frequency Matrix
Amino Acid Modal Frequencies
Amino Acid Modal Sequence
Amino Acid Second Modal Frequency
Specimen Nucleotide Frequencies
Convert Amino Acid Matrix
VLF position count
VLF Specimen Count
Amino Acid Reduced
Amino Acid Changes
Matching Amino Acid Positions
Amino Acid VLF Analysis Function
Compare VLFs within Species
VLF Concordance Check Function
Concordant Residue Changes
First Modal Conserved
First and Second Modal Conserved
Nucleotide Count
VLF Decile Plot
Error Rate
Read Fasta Files
Frequency Matrix
Find Matching ntVLF and aaVLF Specimen.
Single and Shared VLF Find
Codon Position of Matching aa and ntVLFs
Modal Frequencies
Modal Sequence
Second Modal Frequency
Matching Nucleotide Positions
Final Matching
Separate Specimen by Species Names
Sliding Window
Specimen Nucleotide Frequencies
Frequency Matrix Approach for Assessing Very Low Frequency Variants in...
Amino Acid VLFs
VLF Matrix Convert
VLF Count for Sequence Positions
VLF Count for Specimens
Nucleotide VLF Convert
Reduced VLF Matrix
Nucleotide VLF Assessment Function
Using frequency matrices, very low frequency variants (VLFs) are assessed for amino acid and nucleotide sequences. The VLFs are then compared to see if they occur in only one member of a species, singleton VLFs, or if they occur in multiple members of a species, shared VLFs. The amino acid and nucleotide VLFs are then compared to see if they are concordant with one another. Amino acid VLFs are also assessed to determine if they lead to a change in amino acid residue type, and potential changes to protein structures. Based on Stoeckle and Kerr (2012) <doi:10.1371/journal.pone.0043992> and Phillips et al. (2023) <doi:10.3897/BDJ.11.e96480>.