Limits...
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 .

Show MeSH
Clustering. Phylogenetic clustering of european HIV-1 subtypes
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig3: Clustering. Phylogenetic clustering of european HIV-1 subtypes

Mentions: HIV subtyping HIV gene sequencing and phylogenetic inference is used to identify and classify HIV-1 subtypes [7], and phylogenetic clustering has proven to be a powerful tool to understand the forces that shape patterns of viral sequence diversity [11]. In the following example the clustering algorithm is executed on an HIV-1 tree resulting in a divided and clustered representation that reveals the different subtypes it holds (Fig. 3).Fig. 3


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

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

Clustering. Phylogenetic clustering of european HIV-1 subtypes
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig3: Clustering. Phylogenetic clustering of european HIV-1 subtypes
Mentions: HIV subtyping HIV gene sequencing and phylogenetic inference is used to identify and classify HIV-1 subtypes [7], and phylogenetic clustering has proven to be a powerful tool to understand the forces that shape patterns of viral sequence diversity [11]. In the following example the clustering algorithm is executed on an HIV-1 tree resulting in a divided and clustered representation that reveals the different subtypes it holds (Fig. 3).Fig. 3

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