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Treelink: data integration, clustering and visualization of phylogenetic trees.

Allende C, Sohn E, Little C - BMC Bioinformatics (2015)

Bottom Line: In many of these studies, tree nodes need to be associated with a variety of attributes.For example, in studies concerned with viral relationships, tree nodes are associated with epidemiological information, such as location, age and subtype.Our software can successfully integrate phylogenetic trees with different data sources, and perform operations to differentiate and visualize those differences within a tree.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Engineering and Sciences, Universidad Adolfo Ibañez, Diagonal las Torres 2640, Santiago, 7941169, Chile. christian.allende.cid@gmail.com.

ABSTRACT

Background: Phylogenetic trees are central to a wide range of biological studies. In many of these studies, tree nodes need to be associated with a variety of attributes. For example, in studies concerned with viral relationships, tree nodes are associated with epidemiological information, such as location, age and subtype. Gene trees used in comparative genomics are usually linked with taxonomic information, such as functional annotations and events. A wide variety of tree visualization and annotation tools have been developed in the past, however none of them are intended for an integrative and comparative analysis.

Results: Treelink is a platform-independent software for linking datasets and sequence files to phylogenetic trees. The application allows an automated integration of datasets to trees for operations such as classifying a tree based on a field or showing the distribution of selected data attributes in branches and leafs. Genomic and proteonomic sequences can also be linked to the tree and extracted from internal and external nodes. A novel clustering algorithm to simplify trees and display the most divergent clades was also developed, where validation can be achieved using the data integration and classification function. Integrated geographical information allows ancestral character reconstruction for phylogeographic plotting based on parsimony and likelihood algorithms.

Conclusion: Our software can successfully integrate phylogenetic trees with different data sources, and perform operations to differentiate and visualize those differences within a tree. File support includes the most popular formats such as newick and csv. Exporting visualizations as images, cluster outputs and genomic sequences is supported. Treelink is available as a web and desktop application at http://www.treelinkapp.com .

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Phylogeographic plotting. HIV subtype B consensus tree plotted in Central and South America
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Fig4: Phylogeographic plotting. HIV subtype B consensus tree plotted in Central and South America

Mentions: Phylogeography Phylogeography studies the historical processes that could be responsible for geographic distributions of individuals [12]. In this example an HIV subtype B consensus tree was linked to a dataset that contained the countries of each sequence. Ancestral character reconstruction was performed by a maximum parsimony algorithm [13] that assigned states for the ancestral nodes. Then the result was linked and plotted on a geographical map to visualize the movement of country states in accordance to the tree structure (Fig. 4).Fig. 4


Treelink: data integration, clustering and visualization of phylogenetic trees.

Allende C, Sohn E, Little C - BMC Bioinformatics (2015)

Phylogeographic plotting. HIV subtype B consensus tree plotted in Central and South America
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4696249&req=5

Fig4: Phylogeographic plotting. HIV subtype B consensus tree plotted in Central and South America
Mentions: Phylogeography Phylogeography studies the historical processes that could be responsible for geographic distributions of individuals [12]. In this example an HIV subtype B consensus tree was linked to a dataset that contained the countries of each sequence. Ancestral character reconstruction was performed by a maximum parsimony algorithm [13] that assigned states for the ancestral nodes. Then the result was linked and plotted on a geographical map to visualize the movement of country states in accordance to the tree structure (Fig. 4).Fig. 4

Bottom Line: In many of these studies, tree nodes need to be associated with a variety of attributes.For example, in studies concerned with viral relationships, tree nodes are associated with epidemiological information, such as location, age and subtype.Our software can successfully integrate phylogenetic trees with different data sources, and perform operations to differentiate and visualize those differences within a tree.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Engineering and Sciences, Universidad Adolfo Ibañez, Diagonal las Torres 2640, Santiago, 7941169, Chile. christian.allende.cid@gmail.com.

ABSTRACT

Background: Phylogenetic trees are central to a wide range of biological studies. In many of these studies, tree nodes need to be associated with a variety of attributes. For example, in studies concerned with viral relationships, tree nodes are associated with epidemiological information, such as location, age and subtype. Gene trees used in comparative genomics are usually linked with taxonomic information, such as functional annotations and events. A wide variety of tree visualization and annotation tools have been developed in the past, however none of them are intended for an integrative and comparative analysis.

Results: Treelink is a platform-independent software for linking datasets and sequence files to phylogenetic trees. The application allows an automated integration of datasets to trees for operations such as classifying a tree based on a field or showing the distribution of selected data attributes in branches and leafs. Genomic and proteonomic sequences can also be linked to the tree and extracted from internal and external nodes. A novel clustering algorithm to simplify trees and display the most divergent clades was also developed, where validation can be achieved using the data integration and classification function. Integrated geographical information allows ancestral character reconstruction for phylogeographic plotting based on parsimony and likelihood algorithms.

Conclusion: Our software can successfully integrate phylogenetic trees with different data sources, and perform operations to differentiate and visualize those differences within a tree. File support includes the most popular formats such as newick and csv. Exporting visualizations as images, cluster outputs and genomic sequences is supported. Treelink is available as a web and desktop application at http://www.treelinkapp.com .

Show MeSH