PhyloTraVis: A New Approach to Visualization of the Phylogenetic Tree

Forghani, Majid; Vasev, Pavel; Bolkov, Mikhail A.; Ramsay, Edward; Bersenev, Alexander

doi:10.1134/s0361768822030045

Cited by 1 publication

(4 citation statements)

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“…As mentioned, the pipeline is an extended version of our recent work on visualization of the phylogenetic tree called PhyloTraVis [11]. PhyloTraVis focuses on visualization of evolutionary trajectories defined within a phylogenetic tree.…”

Section: Methodsmentioning

confidence: 99%

“…The first and second steps of the pipeline are related to phylogenetic analysis and are carried out using Randomized Axelerated Maximum Likelihood (RAxML) [14], as described earlier [11]. Here, we focus on further steps related to the embedding and visualization.…”

Section: Methodsmentioning

confidence: 99%

“…Indeed, 𝐶 gives the coordinates of vertices of 𝑉 , while 𝑃 determines how vertices are connected in the space. Before visualization, all paths are smoothed by the Bezier curve algorithm, which has been described in more detail elsewhere [11]. The smoothed path information is passed into Vrungel to visualize the graph.…”

Section: Methodsmentioning

confidence: 99%

“…As an extension of our previous work on phylogenetic tree visualization [1,11], we propose a novel visualization in this paper. In it, the phylogenetic relationships between tree nodes are maintained, whereas the distance between two nodes is determined using Word2Vec encoding and SAAA.…”

Section: Introductionmentioning

confidence: 99%

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Visualization of the Evolutionary Trajectory: Application of Reduced Amino Acid Alphabets and Word2Vec Embedding

Forghani

Firstkov

Vasev

et al. 2022

Proceedings of the 32nd International Conference on Computer Graphics and Vision

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Analysis of viral evolution is a key element of epidemiological surveillance and control. One of the fundamental tools which is widely used to illustrate evolutionary history is the phylogenetic tree. Recently, we have proposed an alternative visualization for the phylogenetic tree using the evolutionary trajectory of its taxa. An evolutionary trajectory is a path starting from a taxon and ending at the root of the tree. In this paper, we propose an embedding of tree nodes by encoding their genetic sequence using a reduced amino acid alphabet and employing the Word2Vec framework. The suggested visualization maintains the phylogenetic relationship between nodes, while their proximity in 3D space depends on three factors: the type of reduced amino acid alphabet; fixed-length genetic patterns used in Word2Vec; and the neighbor effect of adjacent signatures. The results of our experiments showed that the majority of evolutionary history can be described in the embedded space. Moreover, they suggest potential application of our approach as an explanatory tool in studying various aspects: evolutionary dynamics; evolutionary deviation of viral variants; and phylogenetic characteristics, such as formation of new clades. Besides the usual local analysis of point mutations, the developed framework enables studying these aspects based on a more comprehensive global context, including neighboring effects, genetic signatures.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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