The outputs of phylogenetic software are mostly in non-standard formats and not compatible with each other. This restricts the integration and comparative analysis in downstream applications. To address this issue, we developed the treeio, which allows for parsing of standard and a dozen of non-standard data formats, and enables integration of external data. It also supports exporting the phylogenetic tree and related data into a single file. The ability to support input and output means that data format conversion is possible, thereby making more software indirectly support a wider range of data. The parsing and integration of various types of data provides the potential for downstream integrated analyses and comparative analyses, while expanding the scope of application of phylogenetic analysis. This work has been published in Molecular Biology and Evolution 2020 (ESI highly cited).
+The outputs of phylogenetic software are mostly in non-standard formats and not compatible with each other. This restricts the integration and comparative analysis in downstream applications. To address this issue, we developed the treeio, which allows for parsing of standard and a dozen of non-standard data formats, and enables integration of external data. It also supports exporting the phylogenetic tree and related data into a single file. The ability to support input and output means that data format conversion is possible, thereby making more software indirectly support a wider range of data. The parsing and integration of various types of data provides the potential for downstream integrated analyses and comparative analyses, while expanding the scope of application of phylogenetic analysis. This work has been published in Molecular Biology and Evolution 2020 (ESI highly cited).
Two general methods have been proposed and implemented, covering all aspects of the integration and visualization of phylogenetic data. The first method allows data to be mapped to the topology of the tree and supports the direct display of data or its mapping as visualization features; the second method reorganizes external data according to the tree topology, visualizes it in the manner specified by the user, and finally aligns the visualization result with the phylogenetic tree. These two general methods allow various heterogeneous data from different disciplines to be deciphered in the context of phylogenetics, which can contribute to the discovery of new patterns related or the proposal of new hypotheses. This work was published in Molecular Biology and Evolution in 2018. Based on this, the ggtreeExtra package was developed to enhance the integration and visualization capabilities of richly annotated data and was published in Molecular Biology and Evolution in 2021.
+Two general methods have been proposed and implemented, covering all aspects of the integration and visualization of phylogenetic data. The first method allows data to be mapped to the topology of the tree and supports the direct display of data or its mapping as visualization features; the second method reorganizes external data according to the tree topology, visualizes it in the manner specified by the user, and finally aligns the visualization result with the phylogenetic tree. These two general methods allow various heterogeneous data from different disciplines to be deciphered in the context of phylogenetics, which can contribute to the discovery of new patterns related or the proposal of new hypotheses. This work was published in Molecular Biology and Evolution in 2018. Based on this, the ggtreeExtra package was developed to enhance the integration and visualization capabilities of richly annotated data and was published in Molecular Biology and Evolution in 2021.
Visualisation of phylogenetic trees is usually in the form of images, and the corresponding trees and data cannot be reused, which hampers the integration of phylogenetic knowledge and comparative analysis. Studies have shown that about 60% of the published phylogenetic data is permanently lost. To solve this problem, we designed the ggtree object, which encompasses the phylogenetic tree, data, and visualisation directives. It can be rendered into an image, while the phylogenetic tree and related data can be extracted from it. In addition, similar to the “format painter,” the visualization directives can be used for visualizing other tree objects. This work was published in iMeta 2022, supporting data reusability and research replicability while promoting the integration and comparative analysis of phylogenetic data in the field.
+Visualisation of phylogenetic trees is usually in the form of images, and the corresponding trees and data cannot be reused, which hampers the integration of phylogenetic knowledge and comparative analysis. Studies have shown that about 60% of the published phylogenetic data is permanently lost. To solve this problem, we designed the ggtree object, which encompasses the phylogenetic tree, data, and visualisation directives. It can be rendered into an image, while the phylogenetic tree and related data can be extracted from it. In addition, similar to the “format painter,” the visualization directives can be used for visualizing other tree objects. This work was published in iMeta 2022, supporting data reusability and research replicability while promoting the integration and comparative analysis of phylogenetic data in the field.