Live neighbor-joining

BMC Bioinformatics
Guilherme P TellesNalvo F Almeida

Abstract

In phylogenetic reconstruction the result is a tree where all taxa are leaves and internal nodes are hypothetical ancestors. In a live phylogeny, both ancestral and living taxa may coexist, leading to a tree where internal nodes may be living taxa. The well-known Neighbor-Joining heuristic is largely used for phylogenetic reconstruction. We present Live Neighbor-Joining, a heuristic for building a live phylogeny. We have investigated Live Neighbor-Joining on datasets of viral genomes, a plausible scenario for its application, which allowed the construction of alternative hypothesis for the relationships among virus that embrace both ancestral and descending taxa. We also applied Live Neighbor-Joining on a set of bacterial genomes and to sets of images and texts. Non-biological data may be better explored visually when their relationship in terms of content similarity is represented by means of a phylogeny. Our experiments have shown interesting alternative phylogenetic hypothesis for RNA virus genomes, bacterial genomes and alternative relationships among images and texts, illustrating a wide range of scenarios where Live Neighbor-Joining may be used.

References

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Citations

May 18, 2020·International Journal of Systematic and Evolutionary Microbiology·Kui DongJianguo Xu
Jan 12, 2021·Molecular Therapy. Nucleic Acids·Yan HongJuan Wang
Nov 17, 2020·Frontiers in Genetics·Ruth Davidson, Abraham Martín Del Campo

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Datasets Mentioned

BETA
KJ776791
FJ621583
AF5222874

Software Mentioned

bzip2
PROTDIST
GNU
LNJ
Orthologsorter
MUMi
MUMmer
NJ
D3
Live Phylogeny

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