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Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study

Arjun Bhutkar12*, William M Gelbart2 and Temple F Smith1

Author Affiliations

1 BioMolecular Engineering Research Center, Boston University, Cummington St, Boston, MA 02215, USA

2 Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 021383, USA

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Genome Biology 2007, 8:R236  doi:10.1186/gb-2007-8-11-r236

Published: 8 November 2007

Additional files

Additional data file 1:

Filtered list of genes common to all Drosophila species in set (high confidence placements).

Format: TXT Size: 75KB Download file

Open Data

Additional data file 2:

NGPs based on common gene set (in file 1) with arm indexing and only within Drosophila species (without outgroup pairs) - used in clustering of fly species (Figure 1a).

Format: TXT Size: 310KB Download file

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Additional data file 3:

NGPs without arm indexing (to allow for NGPs from outgroup species with varying chromosome architecture) based on Drosophila common gene set (in file 1) - used in the rearrangement and ancestral gene order analysis.

Format: TXT Size: 576KB Download file

Open Data

Additional data file 4:

Clustering results for Figure 1(a)

Format: TXT Size: 3KB Download file

Open Data

Additional data file 5:

Clustering results for Figure 1(b).

Format: TXT Size: 5KB Download file

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Additional data file 6:

Ancestral adjacencies (blocks) at the Drosophila root under criterion 1

Format: TXT Size: 60KB Download file

Open Data

Additional data file 7:

Ancestral adjacencies (blocks) at the Drosophila root under criterion 2.

Format: TXT Size: 60KB Download file

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Additional data file 8:

Summary of results of testing with the mitochondrial test dataset.

Format: PDF Size: 33KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional data file 9:

Tree file from PHYLIP version 3.65 for SRP54 and SRP19 gene sequences used for Figure 2.

Format: TXT Size: 1KB Download file

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Additional data file 10:

Detailed description of the method.

Format: PDF Size: 49KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data