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MIPhy: Identify and quantify rapidly evolving members of large gene families

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RT @jdwasmuth: Trying to make sense of your large, complex gene family? Check out MIPhy by @DaveAScientist. Preprint in @PeerJPreprints htt…
RT @jdwasmuth: Trying to make sense of your large, complex gene family? Check out MIPhy by @DaveAScientist. Preprint in @PeerJPreprints htt…
MIPhy: Identify and quantify rapidly evolving members of large gene families https://t.co/9cp7VWSQoS
Trying to make sense of your large, complex gene family? Check out MIPhy by @DaveAScientist. Preprint in @PeerJPreprints https://t.co/EHamxGneeJ #Bioinformatics #ComputationalBiology #EvolutionaryStudies
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Supplemental Information

Supporting information

Table S1: The nematode collagens identified in this work from species in the genus Caenorhabditis.

Article S1. The MIPhy model of gene family evolution.

Figure S1: Example species and gene trees.

DOI: 10.7287/peerj.preprints.26593v1/supp-1

Data from collagen analysis

The following files are contained in the tarball:

all_caen.col2.fas - collagen sequences from seven species of Caenorhabditis in fasta format.

MIPhy_scores.csv - comma separated file generated by MIPhy. (1) sequence identifier; (2) species identifier; (3) MIPhy cluster identifier; (4) Instability score.

withPheno.txt - MIPhy clusters that contained a C. elegans collagen with a major RNAi phenotype. (1) MIPhy cluster identifier; (2) Instability score.

withoutPheno.txt - MIPhy clusters that contained no C. elegans collagens with a major RNAi phenotype. (1) MIPhy cluster identifier; (2) Instability score.

DOI: 10.7287/peerj.preprints.26593v1/supp-2

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

David M Curran conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

John S Gilleard conceived and designed the experiments, authored or reviewed drafts of the paper, approved the final draft.

James D Wasmuth conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

MIPhy is freely available https://github.com/dave-the-scientist/miphy under a BSD 2-clause license.

It is also available as an online tool at http://miphy.wasmuthlab.org.

Funding

This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) through a Discovery Grant (#06239-2015) to JDW, a Collaborative Research and Training Experience Program (CREATE) program in Host-Parasite Interactions (#413888-2012) to JDW and JSG (and others), and by Alberta Innovates – Technology Futures through a doctoral scholarship to DMC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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