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MixTreEM specifications

Information


Unique identifier OMICS_13052
Name MixTreEM
Alternative name Mixture of Trees using Expectation Maximization
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Gene families sequences
Output data Synthetic gene families as species tree
Operating system Unix/Linux, Windows
Programming languages C++
Parallelization MPI
Computer skills Advanced
Stability Stable
Source code URL http://prime.scilifelab.se/mixtreem/downloads/mixtreem_source.tar.gz
Maintained Yes

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  • person_outline Jens Lagergren <>

Publication for Mixture of Trees using Expectation Maximization

MixTreEM in publications

 (2)
PMCID: 5123345
PMID: 28185583
DOI: 10.1186/s12859-016-1268-2

[…] [, ]. species-tree aware methods are sensitive to errors in reconstructed species trees; however, resources such as timetree [] and recent species tree reconstruction methods, such as phyldog and mixtreem [, ], appears to be sufficiently reliable., for future work, extending the model to incorporate even more biological knowledge is of interest. in particular, being able to distinguish […]

PMCID: 4603753
PMID: 26450506
DOI: 10.1186/1471-2164-16-S10-S1

[…] are also methods designed to infer species trees in the presence of gene tree discordance resulting from duplication and loss, and it is possible that some of these methods (e.g., phyldog [] and mixtreem []) might have good accuracy under the msc. future work should also explore ca-ml using different ml heuristics (e.g., phyml [], nhphyml [], iqtree []) and under more complex sequence […]


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MixTreEM 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
MixTreEM 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)

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