Open Access Highly Accessed Research article

The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences

Ralph S Peters1*, Benjamin Meyer2, Lars Krogmann3, Janus Borner4, Karen Meusemann1, Kai Schütte5, Oliver Niehuis1 and Bernhard Misof1

Author Affiliations

1 Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, D-53113 Bonn, Germany

2 Institut für Systemische Neurowissenschaften, Universitätsklinikum Hamburg-Eppendorf, Martinistrasse 52, D-20246 Hamburg, Germany

3 Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, D-70191 Stuttgart, Germany

4 Zoologisches Institut der Universität Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany

5 Zoologisches Museum Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany

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BMC Biology 2011, 9:55  doi:10.1186/1741-7007-9-55

Published: 18 August 2011

Additional files

Additional file 1:

Software tools and manuals. All newly developed software tools and corresponding manuals.

Format: ZIP Size: 44KB Download file

Open Data

Additional file 2:

gi numbers of sequences from GenBank used in our pipeline. List of the GenBank gi numbers of all Hymenoptera sequences that were initially inputted in our pipeline run.

Format: TXT Size: 1.4MB Download file

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Additional file 3:

On maximum cliques. A short introduction to maximum cliques and how we used them in our analysis.

Format: PDF Size: 135KB Download file

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Additional file 4:

Character partitions of subset 1 and 2. The character partitions of the two subsets that were used in the phylogenetic analyses (subset 1 and subset 2).

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Additional file 5:

Tree 1, complete. Phylogenetic tree of Hymenoptera inferred from GenBank sequences (tree 1). Numbers on branches indicate bootstrap support values (%). The applied color code corresponds to that of Figures 2 and 3. Single species whose position in the inferred phylogenetic tree we consider erroneous are shown in gray.

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Additional file 6:

Tree 2, complete. Phylogenetic tree of Hymenoptera inferred from GenBank sequences (tree 2). In this tree, species that were excluded by our pipeline in the course of generating subset 1 are reincluded. These taxa are marked with asterisks. The meaning of numbers and the applied color code correspond to those in Additional file 5.

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Additional file 7:

Species included in subset 1. All species included in subset 1, sorted by family.

Format: TXT Size: 40KB Download file

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Additional file 8:

Groups of orthologs included in subset 1. All groups of orthologs included in subset 1, plus coverage of each group.

Format: TXT Size: 6KB Download file

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Additional file 9:

Species included in subset 2. All species included in subset 2, sorted by family.

Format: TXT Size: 42KB Download file

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Additional file 10:

Groups of orthologs included in subset 2. All groups of orthologs included in subset 2, plus coverage of each group.

Format: TXT Size: 6KB Download file

Open Data