TY  - JOUR
AB  - Background

The increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of phylogenies—a challenging task if close reference sequences are not available, genome sequences are incompletely assembled, or the high number of genomes precludes multiple sequence alignment in reasonable time.
Results

We present a new whole-genome based approach to infer phylogenies that is alignment- and reference-free. In contrast to other methods, it does not rely on pairwise comparisons to determine distances to infer edges in a tree. Instead, a colored de Bruijn graph is constructed, and information on common subsequences is extracted to infer phylogenetic splits.
Conclusions

The introduced new methodology for large-scale phylogenomics shows high potential. Application to different datasets confirms robustness of the approach. A comparison to other state-of-the-art whole-genome based methods indicates comparable or higher accuracy and efficiency.
DA  - 2020
DO  - 10.1186/s13015-020-00164-3
KW  - Computational Theory and Mathematics
KW  - Applied Mathematics
KW  - Molecular Biology
KW  - Structural Biology
LA  - eng
IS  - 1
PY  - 2020
T2  - Algorithms for Molecular Biology
TI  - Alignment- and reference-free phylogenomics with colored de Bruijn graphs
UR  - https://nbn-resolving.org/urn:nbn:de:0070-pub-29424214
Y2  - 2024-11-22T07:57:53
ER  -