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Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython

Eric Talevich1*, Brandon M Invergo2, Peter JA Cock3 and Brad A Chapman4

Author Affiliations

1 Institute of Bioinformatics, University of Georgia, 120 Green Street, Athens, GA 30602, USA

2 Institute of Evolutionary Biology (CSIC-UPF), CEXS-UPF-PRBB, C/ Doctor Aiguader 88, 08003 Barcelona, Spain

3 James Hutton Institute, InvergowrieDundee DD2 5DA, UK

4 Harvard School of Public Health Bioinformatics Core, 655 Huntington Ave, Boston, MA 02115, USA

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BMC Bioinformatics 2012, 13:209  doi:10.1186/1471-2105-13-209

Published: 21 August 2012

Additional files

Additional file 1:

Tree rerooting. Example code to read a tree from a file and write copies of the tree rerooted at every internal and external node. The method find_clades produces an iterator over the tree rather than a new list, in order to make more efficient use of memory in general. In this case, because the method root_with_outgroup modifies the tree in-place, which could change the ordering of nodes during traversal, list is used to create an unchanging copy of references to the original nodes in the tree.

Format: PY Size: 1KB Download file

Open Data

Additional file 2:

Performance benchmark script. Python script to time the execution of the benchmark tasks shown in Table 2.

Format: PY Size: 5KB Download file

Open Data