Dataset Information

TreeSnatcher plus: capturing phylogenetic trees from images.

ABSTRACT:

Background

Figures of phylogenetic trees are widely used to illustrate the result of evolutionary analyses. However, one cannot easily extract a machine-readable representation from such images. Therefore, new software emerges that helps to preserve phylogenies digitally for future research.

Results

TreeSnatcher Plus is a GUI-driven JAVA application that semi-automatically generates a Newick format for multifurcating, arbitrarily shaped, phylogenetic trees contained in pixel images. It offers a range of image pre-processing methods and detects the topology of a depicted tree with adequate user assistance. The user supervises the recognition process, makes corrections to the image and to the topology and repeats steps if necessary. At the end TreeSnatcher Plus produces a Newick tree code optionally including branch lengths for rectangular and freeform trees.

Conclusions

Although illustrations of phylogenies exist in a vast number of styles, TreeSnatcher Plus imposes no limitations on the images it can process with adequate user assistance. Given that a fully automated digitization of all figures of phylogenetic trees is desirable but currently unrealistic, TreeSnatcher Plus is the only program that reliably facilitates at least a semi-automatic conversion from such figures into a machine-readable format.

SUBMITTER: Laubach T

PROVIDER: S-EPMC3411374 | biostudies-literature | 2012 May

REPOSITORIES: biostudies-literature

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Publications

TreeSnatcher plus: capturing phylogenetic trees from images.

Laubach Thomas T von Haeseler Arndt A Lercher Martin J MJ

BMC bioinformatics 20120524

<h4>Background</h4>Figures of phylogenetic trees are widely used to illustrate the result of evolutionary analyses. However, one cannot easily extract a machine-readable representation from such images. Therefore, new software emerges that helps to preserve phylogenies digitally for future research.<h4>Results</h4>TreeSnatcher Plus is a GUI-driven JAVA application that semi-automatically generates a Newick format for multifurcating, arbitrarily shaped, phylogenetic trees contained in pixel image ...[more]

PMID: 22624611

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Project description:Phylogenetic analysis is used to analyze the evolution of species according to the characteristics of biological sequences. The analytical results are generally represented by phylogenetic trees. NJ (neighbor joining) is a frequently used algorithm for constructing phylogenetic trees because of its few assumptions, fast operation, and high accuracy, and is based on the distance between taxa. It is known that NJ usually constructs different phylogenetic trees for the same dataset with differences in input order, which are known as “tied trees.” This article proposes an improved method of NJ, called ENJ (extended neighbor joining). The ENJ can join several (currently limited to three) nodes with the same minimum distance into a new node, rather than joining two nodes in one iteration, so it can construct triple phylogenetic trees. We have inferred the formulas for updating the distance values and calculating the branch lengths for the ENJ algorithm. We have tested the ENJ with simulated and real data. The experimental results show that, compared with other methods, the trees constructed by the ENJ have greater similarity to the initial trees, and the ENJ is much faster than the NJ algorithm. Moreover, we have constructed a phylogenetic tree for the novel coronavirus (COVID-19) and related coronaviruses by ENJ, which shows that COVID-19 and SARS-CoV are closer than other coronaviruses. Because it differs from the existing phylogenetic trees for those coronaviruses, we constructed a phylogenetic network for them. The network shows those species have had a reticulate evolution. Graphical Abstract Accurately inferring evolutionary relationships between species can help humans to understand the evolutionary history and the mechanism. ENJ is an efficient and effective algorithm for constructing phylogenetic trees, which can construct triple phylogenetic trees, if necessary. The trees constructed by ENJ can better describe the original information and reflect the real evolutionary relationship of species.

Dataset Information

TreeSnatcher plus: capturing phylogenetic trees from images.

Background

Results

Conclusions

Publications

TreeSnatcher plus: capturing phylogenetic trees from images.

Similar Datasets

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