PhyBin: binning trees by topology

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PeerJ

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Introduction

Method and Implementation

Generating orthologous sets and input trees

Description of the Program

Fast binning mode

Pre-processing data

Full clustering mode using Robinson-Foulds distance matrix

Output formats

Performance

Results and Discussion

Supplemental Information

Cluster membership changes as a result of hierarchical clustering options

The number of clusters and cluster membership when PhyBin is run on the Wolbachia ortholog set (503 trees total, –editdist=3) using single linkage (–single), UPGMA (–UPGMA [default]), or complete linkage (–complete) hierarchical clustering.

DOI: 10.7717/peerj.187/supp-1

Additional Information and Declarations

Competing Interests

Irene Newton is an Academic Editor for PeerJ.

Author Contributions

Ryan R. Newton performed the experiments, contributed reagents/materials/analysis tools, wrote the paper.

Irene L.G. Newton conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper.

Data Deposition

DDBJ: wVitA: PRJDB1504; wUni: PRJNA33275.

Funding

Funding was provided by a generous laboratory startup given to ILGN by Indiana University. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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