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A classification guide tree is used to help the group division process.
The aligners MLAGAN, TBA, and PECAN require specification of a guide tree for alignment; a guide tree is optional for MAVID.
The resulting tree is midpoint-rooted to yield our progressive anchoring guide tree.
For multiple genome comparisons, a guide tree is used to determine the alignment order.
Our method computes alignment anchors progressively according to a guide tree computed as follows.
Aligned sequences were inserted into the SSURef SILVA guide tree using the parsimony insertion function of ARB [59].
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These sequence families expose progressive methods to guide-tree bias.
The generated guide-tree was then visualized with Geneious.
A method highly dependent of the guide-tree may result in accurate or inaccurate alignments given the correct guide-tree.
To test the extent to which gap patterns follow the guide-tree, we measured the effect of altering the guide-tree.
In this framework, a high level of guide-tree dependency will produce trees that are close to the guide-tree, thus maximizing the distance in the mentioned space.
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