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Mixture of Trees using Expectation Maximization MixTreEM

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A package to reconstruct species tree. MixTreEM uses a probabilistic generative mixture model to reconstruct a set of k-candidate species trees given a set of n monocopy gene families. In the first phase, a set of probable species trees are inferred given gene family data. In the second phase, each of the species tree, along with the gene families, is fed into DLRS (Duplication, Loss, Rate and Sequence) model, ultimately giving us the best species tree.

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MixTreEM classification

MixTreEM specifications

Software type:
Package/Module
Restrictions to use:
None
Output data:
Synthetic gene families as species tree
Programming languages:
C++
Computer skills:
Advanced
Source code URL:
http://prime.scilifelab.se/mixtreem/downloads/mixtreem_source.tar.gz
Interface:
Command line interface
Input data:
Gene families sequences
Operating system:
Unix/Linux, Windows
Parallelization:
MPI
Stability:
Stable
Maintained:
Yes

MixTreEM distribution

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MixTreEM support

Maintainer

  • Jens Lagergren <>

Credits

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Publications

Institution(s)

School of Computer Science and Communication, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, Espoo, Finland; School of Computer Science and Communication, Science for Life Laboratory, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden

Funding source(s)

Swedish e-Science Research Center, The Swedish Research Council (2010-4757), University of Engineering and Technology, Peshawar, Pakistan and the Academy of Finland (Finnish Centre of Excellence in Computational Inference Research COIN, 251170)

Link to literature

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