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Supplemental Information

Supplemental Note 1: Summary of CAM Options

A short summary of available parameters to modify the output from CAM.

DOI: 10.7287/peerj.preprints.27756v1/supp-1

The advantages and disadvantages of each phylogenetic comparison metric

The first column is the name of the metric. The second column is a short description of how the metric works. The third and fourth columns explain the advantages and disadvantages of each method, respectively.

DOI: 10.7287/peerj.preprints.27756v1/supp-2

Frequency of Partial Genes

This figure shows the proportion of partial genes in each clade. A partial gene is defined as a gene in which we do not have the entire DNA sequence available. Each boxplot represents the distribution of the proportion of partial genes in each species of the clade.

DOI: 10.7287/peerj.preprints.27756v1/supp-3

All Clades - Motifs Found in Multiple Species vs. Unique Motifs

Shows how many motifs are shared in different genes within the same clade versus how many motifs are unique to a single gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-4

Archaea - Motifs Found in Multiple Species vs. Unique Motifs

Shows how many motifs are shared in different genes within the same clade versus how many motifs are unique to a single gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-5

Bacteria - Motifs Found in Multiple Species vs. Unique Motifs

Shows how many motifs are shared in different genes within the same clade versus how many motifs are unique to a single gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-6

Fungi - Motifs Found in Multiple Species vs. Unique Motifs

Shows how many motifs are shared in different genes within the same clade versus how many motifs are unique to a single gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-7

Invertebrates - Motifs Found in Multiple Species vs. Unique Motifs

Shows how many motifs are shared in different genes within the same clade versus how many motifs are unique to a single gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-8

Mammals - Motifs Found in Multiple Species vs. Unique Motifs

Shows how many motifs are shared in different genes within the same clade versus how many motifs are unique to a single gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-9

Plants - Motifs Found in Multiple Species vs. Unique Motifs

Shows how many motifs are shared in different genes within the same clade versus how many motifs are unique to a single gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-10

Protozoa - Motifs Found in Multiple Species vs. Unique Motifs

Shows how many motifs are shared in different genes within the same clade versus how many motifs are unique to a single gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-11

Vertebrate Other - Motifs Found in Multiple Species vs. Unique Motifs

Shows how many motifs are shared in different genes within the same clade versus how many motifs are unique to a single gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-12

Viruses - Motifs Found in Multiple Species vs. Unique Motifs

Shows how many motifs are shared in different genes within the same clade versus how many motifs are unique to a single gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-13

All Clades - Frequency of Codon Aversion by Codon

The frequency of codon exclusion for the taxonomic group. The box plot represents the frequency of species in the taxonomic group that exclude a certain codon in their genes (e.g., if a codon is not used in 50% of a species' genes, then that species would be plotted at 0.50).

DOI: 10.7287/peerj.preprints.27756v1/supp-14

Archaea - Frequency of Codon Aversion by Codon

The frequency of codon exclusion for the taxonomic group. The box plot represents the frequency of species in the taxonomic group that exclude a certain codon in their genes (e.g., if a codon is not used in 50% of a species' genes, then that species would be plotted at 0.50).

DOI: 10.7287/peerj.preprints.27756v1/supp-15

Bacteria - Frequency of Codon Aversion by Codon

The frequency of codon exclusion for the taxonomic group. The box plot represents the frequency of species in the taxonomic group that exclude a certain codon in their genes (e.g., if a codon is not used in 50% of a species' genes, then that species would be plotted at 0.50).

DOI: 10.7287/peerj.preprints.27756v1/supp-16

Fungi - Frequency of Codon Aversion by Codon

The frequency of codon exclusion for the taxonomic group. The box plot represents the frequency of species in the taxonomic group that exclude a certain codon in their genes (e.g., if a codon is not used in 50% of a species' genes, then that species would be plotted at 0.50).

DOI: 10.7287/peerj.preprints.27756v1/supp-17

Invertebrates - Frequency of Codon Aversion by Codon

The frequency of codon exclusion for the taxonomic group. The box plot represents the frequency of species in the taxonomic group that exclude a certain codon in their genes (e.g., if a codon is not used in 50% of a species' genes, then that species would be plotted at 0.50).

DOI: 10.7287/peerj.preprints.27756v1/supp-18

Mammals - Frequency of Codon Aversion by Codon

The frequency of codon exclusion for the taxonomic group. The box plot represents the frequency of species in the taxonomic group that exclude a certain codon in their genes (e.g., if a codon is not used in 50% of a species' genes, then that species would be plotted at 0.50).

DOI: 10.7287/peerj.preprints.27756v1/supp-19

Plants - Frequency of Codon Aversion by Codon

The frequency of codon exclusion for the taxonomic group. The box plot represents the frequency of species in the taxonomic group that exclude a certain codon in their genes (e.g., if a codon is not used in 50% of a species' genes, then that species would be plotted at 0.50).

DOI: 10.7287/peerj.preprints.27756v1/supp-20

Protozoa - Frequency of Codon Aversion by Codon

The frequency of codon exclusion for the taxonomic group. The box plot represents the frequency of species in the taxonomic group that exclude a certain codon in their genes (e.g., if a codon is not used in 50% of a species' genes, then that species would be plotted at 0.50).

DOI: 10.7287/peerj.preprints.27756v1/supp-21

Vertebrate Other - Frequency of Codon Aversion by Codon

The frequency of codon exclusion for the taxonomic group. The box plot represents the frequency of species in the taxonomic group that exclude a certain codon in their genes (e.g., if a codon is not used in 50% of a species' genes, then that species would be plotted at 0.50).

DOI: 10.7287/peerj.preprints.27756v1/supp-22

Viruses - Frequency of Codon Aversion by Codon

The frequency of codon exclusion for the taxonomic group. The box plot represents the frequency of species in the taxonomic group that exclude a certain codon in their genes (e.g., if a codon is not used in 50% of a species' genes, then that species would be plotted at 0.50).

DOI: 10.7287/peerj.preprints.27756v1/supp-23

All Clades - Number of Codons Excluded in Motifs

Shows the frequency of how many codons (0-64) are not used in each gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-24

Archaea - Number of Codons Excluded in Motifs

Shows the frequency of how many codons (0-64) are not used in each gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-25

Bacteria - Number of Codons Excluded in Motifs

Shows the frequency of how many codons (0-64) are not used in each gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-26

Fungi - Number of Codons Excluded in Motifs

Shows the frequency of how many codons (0-64) are not used in each gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-27

Invertebrates - Number of Codons Excluded in Motifs

Shows the frequency of how many codons (0-64) are not used in each gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-28

Mammals - Number of Codons Excluded in Motifs

Shows the frequency of how many codons (0-64) are not used in each gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-29

Protozoa - Number of Codons Excluded in Motifs

Shows the frequency of how many codons (0-64) are not used in each gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-30

Plants - Number of Codons Excluded in Motifs

Shows the frequency of how many codons (0-64) are not used in each gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-31

Vertebrate Other - Number of Codons Excluded in Motifs

Shows the frequency of how many codons (0-64) are not used in each gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-32

Viruses - Number of Codons Excluded in Motifs

Shows the frequency of how many codons (0-64) are not used in each gene.

DOI: 10.7287/peerj.preprints.27756v1/supp-33

All Clades - Repeated Motifs

The frequency of which codon motifs are repeated is shown. The x- axis depicts how many time a motif was repeated in all the genes in a clade. The y-axis depicts how many motifs were repeated a given number of times (shown in the natural log). Some outliers were removed from each graph for clarity. These outliers represent the motifs in which only stop codons are excluded. All clades outliers excluded: (1309911,1), (2185083,1), (2433089,1).

DOI: 10.7287/peerj.preprints.27756v1/supp-34

Archaea - Repeated Motifs

The frequency of which codon motifs are repeated is shown. The x- axis depicts how many time a motif was repeated in all the genes in a clade. The y-axis depicts how many motifs were repeated a given number of times (shown in the natural log). Some outliers were removed from each graph for clarity. These outliers represent the motifs in which only stop codons are excluded. Archaea outliers excluded: (10360,1), (10564,1).

DOI: 10.7287/peerj.preprints.27756v1/supp-35

Bacteria - Repeated Motifs

The frequency of which codon motifs are repeated is shown. The x- axis depicts how many time a motif was repeated in all the genes in a clade. The y-axis depicts how many motifs were repeated a given number of times (shown in the natural log). Some outliers were removed from each graph for clarity. These outliers represent the motifs in which only stop codons are excluded. Bacteria outliers excluded: (681998,1), (1085854,1), (1611727,1).

DOI: 10.7287/peerj.preprints.27756v1/supp-36

Fungi - Repeated Motifs

The frequency of which codon motifs are repeated is shown. The x- axis depicts how many time a motif was repeated in all the genes in a clade. The y-axis depicts how many motifs were repeated a given number of times (shown in the natural log). Some outliers were removed from each graph for clarity. These outliers represent the motifs in which only stop codons are excluded. Fungi outliers excluded: (140907,0), (157884,1), (226451,1).

DOI: 10.7287/peerj.preprints.27756v1/supp-37

Invertebrates - Repeated Motifs

The frequency of which codon motifs are repeated is shown. The x- axis depicts how many time a motif was repeated in all the genes in a clade. The y-axis depicts how many motifs were repeated a given number of times (shown in the natural log). Some outliers were removed from each graph for clarity. These outliers represent the motifs in which only stop codons are excluded. Invertebrates outliers excluded: (110662,1), (201864,1), (166597,1).

DOI: 10.7287/peerj.preprints.27756v1/supp-38

Mammals - Repeated Motifs

The frequency of which codon motifs are repeated is shown. The x- axis depicts how many time a motif was repeated in all the genes in a clade. The y-axis depicts how many motifs were repeated a given number of times (shown in the natural log). Some outliers were removed from each graph for clarity. These outliers represent the motifs in which only stop codons are excluded. Mammal outliers excluded: (81051,1), (105156,1), (17812,1).

DOI: 10.7287/peerj.preprints.27756v1/supp-39

Plants - Repeated Motifs

The frequency of which codon motifs are repeated is shown. The x- axis depicts how many time a motif was repeated in all the genes in a clade. The y-axis depicts how many motifs were repeated a given number of times (shown in the natural log). Some outliers were removed from each graph for clarity. These outliers represent the motifs in which only stop codons are excluded. Plants outliers excluded: (158430,1), (127795,1), (224688,1).

DOI: 10.7287/peerj.preprints.27756v1/supp-40

Protozoa - Repeated Motifs

The frequency of which codon motifs are repeated is shown. The x- axis depicts how many time a motif was repeated in all the genes in a clade. The y-axis depicts how many motifs were repeated a given number of times (shown in the natural log). Some outliers were removed from each graph for clarity. These outliers represent the motifs in which only stop codons are excluded. Protozoa Outliers excluded: (32139,1), (41048,1), (30539,1).

DOI: 10.7287/peerj.preprints.27756v1/supp-41

Vertebrate Other - Repeated Motifs

The frequency of which codon motifs are repeated is shown. The x- axis depicts how many time a motif was repeated in all the genes in a clade. The y-axis depicts how many motifs were repeated a given number of times (shown in the natural log). Some outliers were removed from each graph for clarity. These outliers represent the motifs in which only stop codons are excluded. Vertebrate other outliers excluded: (167892,1), (114746,1), (254804,1).

DOI: 10.7287/peerj.preprints.27756v1/supp-42

Viruses - Repeated Motifs

The frequency of which codon motifs are repeated is shown. The x- axis depicts how many time a motif was repeated in all the genes in a clade. The y-axis depicts how many motifs were repeated a given number of times (shown in the natural log). Some outliers were removed from each graph for clarity. These outliers represent the motifs in which only stop codons are excluded. Virus outliers excluded: (2669,1), (2167,1), (4664,1)

DOI: 10.7287/peerj.preprints.27756v1/supp-43

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Justin B Miller conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Lauren M McKinnon performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Michael F Whiting analyzed the data, authored or reviewed drafts of the paper, approved the final draft.

Perry G Ridge analyzed the data, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

CAM is available at https://github.com/ridgelab/cam. All genomes used in our analyses were downloaded from the RefSeq ftp site at ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/.

Funding

Brigham Young University sponsored our research. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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