CAM: An alignment-free method to recover phylogenies using codon aversion motifs
Submission
Authors: Justin Miller, Lauren McKinnon, Michael Whiting, Perry Ridge
Molecular Phylogenetics and Evolution
Submitted: June 18, 2018
Currently Under Review
Novelty of Approach
-CAM uses codon aversion motifs to recover phylogenies without aligning genes.
Results
-CAM is comparable to maximum likelihood in many instances.
-Partial gene annotations do not significantly affect the recovered phylogeny.
-We analyzed 229,742,339 genes from 23,428 species across all kingdoms of life.
Unique Tuples in Each Taxonomic Group
Comparison to Reference Phylogenies
Comparison to Open Tree of Life
Comparison to NCBI Taxonomy
CPU Runtime
Taxonomic Group | CAM | Amino Acid Motifs | FFP | Maximum Likelihood |
All | 17.279 | 20.2692 | 3.907 | N/A |
Archaea | 0.0667 | 0.1436 | 0.041 | 161.5 |
Bacteria | 14.699 | 17.4458 | 3.744 | N/A |
Fungi | 0.0783 | 0.2167 | 0.029 | 199.75 |
Invertebrates | 0.0763 | 0.2126 | 0.045 | 2.5 |
Plants | 0.0781 | 0.2211 | 0.038 | 6 |
Protozoa | 0.0287 | 0.0833 | 0.018 | 4 |
Mammals | 0.0718 | 0.2101 | 0.029 | 2.5 |
Other vertebrates | 0.0872 | 0.2356 | 0.032 | 6.75 |
Viruses | 0.1028 | 0.1161 | 0.102 | N/A |