Display of bootstrap values and rerooting the tree
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lucas...@h-its.org
May 31, 2016, 11:10:24 PM5/31/16
to FigTree Discussion
Hi,
currently, Jaime Cepas, Alexis Stamatakis and I are working on an update to the article "Do Phylogenetic Tree Viewers correctly display Support Values?" (see http://biorxiv.org/content/early/2015/12/25/035360).
In this article, we report an issue about the distinction between values that belong to inner nodes vs those that belong to edges of the tree, for example, bootstrap support values. Our evaluation of FigTree is as follows:
> FigTree is able to display multiple inner node values using both semantic interpretations. Of the tested viewers, it offers the best support for general tree annotation. When re-rooting the tree, however, there is no option to define the interpretation of node labels, since FigTree always assumes the branch interpretation. In addition, it can not parse certain Newick variants, such as trees that contain both, branch lengths, and support values stored as comments.
For details, see our article. We now want to publish an update to this article and where hoping to report that some of those problems could be fixed. Thus, I am opening this issue to report our findings.
If you need more information in order to fix this, let me know.
Lucas
PS: I just tried to post this before, but it did not show up in the list. Sorry if this here results in a duplication.
currently, Jaime Cepas, Alexis Stamatakis and I are working on an update to the article "Do Phylogenetic Tree Viewers correctly display Support Values?" (see http://biorxiv.org/content/early/2015/12/25/035360).
In this article, we report an issue about the distinction between values that belong to inner nodes vs those that belong to edges of the tree, for example, bootstrap support values. Our evaluation of FigTree is as follows:
> FigTree is able to display multiple inner node values using both semantic interpretations. Of the tested viewers, it offers the best support for general tree annotation. When re-rooting the tree, however, there is no option to define the interpretation of node labels, since FigTree always assumes the branch interpretation. In addition, it can not parse certain Newick variants, such as trees that contain both, branch lengths, and support values stored as comments.
For details, see our article. We now want to publish an update to this article and where hoping to report that some of those problems could be fixed. Thus, I am opening this issue to report our findings.
If you need more information in order to fix this, let me know.
Lucas
PS: I just tried to post this before, but it did not show up in the list. Sorry if this here results in a duplication.
lucas...@h-its.org
May 31, 2016, 11:10:25 PM5/31/16
to FigTree Discussion
Hi,
currently, Jaime Cepas, Alexis Stamatakis and I are working on an update to the article "Do Phylogenetic Tree Viewers correctly display Support Values?" (see http://biorxiv.org/content/early/2015/12/25/035360).
In this article, we report an issue about the distinction between values that belong to inner nodes vs those that belong to edges of the tree, for example, bootstrap support values. Our evaluation of FigTree is as follows:
currently, Jaime Cepas, Alexis Stamatakis and I are working on an update to the article "Do Phylogenetic Tree Viewers correctly display Support Values?" (see http://biorxiv.org/content/early/2015/12/25/035360).
In this article, we report an issue about the distinction between values that belong to inner nodes vs those that belong to edges of the tree, for example, bootstrap support values. Our evaluation of FigTree is as follows:
> FigTree is able to display multiple inner node values using both semantic interpretations [that is, values belong to nodes or branches]. Of the tested viewers, it offers the best support for general tree annotation. When re-rooting the tree, however, there is no option to define the interpretation of node labels, since FigTree always assumes the branch interpretation. In addition, it can not parse certain Newick variants, such as trees that contain both, branch lengths, and support values stored as comments.
For details, see the article. We now want to publish an update to this article and where hoping to report that some of those problems could be fixed. Thus, I am opening this issue to report our findings. Do you think this could be fixed in future releases?
For details, see the article. We now want to publish an update to this article and where hoping to report that some of those problems could be fixed. Thus, I am opening this issue to report our findings. Do you think this could be fixed in future releases?
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