Performs comparative expression evolution analysis based on RNA-seq data. TreeExp includes optimized input formatting, normalization, pairwise expression distance estimation, expression character tree inference, and preliminary expression phylogenetic network analysis. It also enables user to map expression distance onto a customized phylogenetic tree.

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TreeExp classification

  • Animals

TreeExp specifications

Software type:
Package
Restrictions to use:
None
Input format:
TXT
Output format:
JPG file
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Input data:
RNAseq data, reads count file
Output data:
Phylogenic tree and distance matrix
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 3.0
Version:
1.2

Publications

  • (Ruan et al., 2016) TreeExp1.0: R Package for Analyzing Expression Evolution Based on RNA-Seq Data. Journal of Experimental Zoology.
    PMID: 27781409

TreeExp support

Documentation

Credits

Institution(s)

State Key Laboratory of Genetic Engineering, MOE Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan; University, Shanghai, China; Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IO, USA

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