MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis

@article{Kumar2012MEGACCCC,
  title={MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis},
  author={Sudhir Kumar and Glen Stecher and Daniel Peterson and Koichiro Tamura},
  journal={Bioinformatics},
  year={2012},
  volume={28 20},
  pages={
          2685-6
        }
}
UNLABELLED There is a growing need in the research community to apply the molecular evolutionary genetics analysis (MEGA) software tool for batch processing a large number of datasets and to integrate it into analysis workflows. Therefore, we now make available the computing core of the MEGA software as a stand-alone executable (MEGA-CC), along with an analysis prototyper (MEGA-Proto). MEGA-CC provides users with access to all the computational analyses available through MEGA's graphical user… 
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References

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MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences
TLDR
The motivation, design principles and priorities that have shaped the development of MEGA are discussed and how MEGA might evolve in the future to assist researchers in their growing need to analyze large data set using new computational methods are discussed.
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.
TLDR
The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
TLDR
UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
Conflict of interests None declared. References
  • 2011
Funding: Research grants from the US National Institutes of Health (HG002096-11 and GM081066-04 to SK) and Japan Society for the Promotion of Science (KT)
  • Funding: Research grants from the US National Institutes of Health (HG002096-11 and GM081066-04 to SK) and Japan Society for the Promotion of Science (KT)