Tree Import
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Background
Being able to import trees from existing tree repository has been identified as an important feature. The main repository identified so far are
- Phylota (http://phylota.net/)
- TreeBase (http://www.treebase.org/)
Phylota is a collection of nucleotide sequences, multiple sequence alignments and trees obtained by querying all the core content of GenBank (i.e. excluding ESTs, STSs, and other kinds of bulk or high-throughput sequences). The MSA are generated through ClustalW or MUSCLE and the tree are built using a fast MP algorithm.
TreeBase in contrast is a repository for published phylogenetic data, containing phylogenetic trees and data matrices.
The 0.3 release of the DE provides the functionality to import tree from Phylota, however the usability is limited by the following factors:
- Incomplete GUI (missing relevant information)
- Extensive polytomies
- Trees have no branch length
1 and 2 could be solved relatively easy, but there is no obvious solution to nr. 3, which limits the analyses that can be performed on these trees. However, Phylota also provides a MSA and if a tree building algorithm were available in the DE, it would be possible for a user to construct a tree with branch length. (Note that the result would be a manual version of the Perpetually Updating Big Plant Tree.)
TreeBase doesn't provide branch length either.
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