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Open Access Highly Accessed Methodology article

Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

Stephen A Smith12*, Jeremy M Beaulieu2 and Michael J Donoghue2

Author Affiliations

1 National Evolutionary Synthesis Center, 2024 W Main St A200, Durham, NC 27705, USA

2 Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT 06520, USA

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BMC Evolutionary Biology 2009, 9:37  doi:10.1186/1471-2148-9-37

Published: 11 February 2009

Additional files

Additional file 1:

Figure S1. The final assembled "guide" tree used to direct the profile alignments across Asterales. Each "terminal" represents the name of the name of the 180-alignment files output from our saturation analysis. We assembled a "guide" tree representing the relationships among the alignment files by compiling and grafting together published phylogenies. This guide tree was then traversed in a post-order manner, performing each profile-to-profile alignment working recursively back to the root.

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Additional file 2:

The "guide" tree used to direct the profile alignments across green plants (Viridiplantae). Similar to Fig S1, each terminal in the tree represents a separate alignment file output from our saturation analysis. Due to the large uncertainty at several nodes, members of a polytomy were profile aligned to find the best order.

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