PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)]
- M. P. Cummings
- Biology
- 15 October 2004
MEGA (Molecular Evolutionary Genetics Analysis)
- M. P. Cummings
- Biology
- 15 October 2004
PHYLIP (Phylogeny Inference Package)
- M. P. Cummings
- Biology
- 15 October 2004
BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics
- Daniel L. Ayres, A. Darling, M. Suchard
- Computer ScienceSystematic Biology
- 1 October 2011
BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference, is presented, which provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms.
GARLI (Genetic Algorithm for Rapid Likelihood Inference)
- M. P. Cummings
- Biology
- 7 April 2014
A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0
- A. Bazinet, Derrick J. Zwickl, M. P. Cummings
- Computer Science, BiologySystematic Biology
- 30 April 2014
Molecularevolution.org, a publicly available gateway for high-throughput, maximum-likelihood phylogenetic analysis powered by grid computing, is introduced and details about how the grid system efficiently delivers high-quality phylogenetic results are provided.
A Genealogical Approach to Quantifying Lineage Divergence
- M. P. Cummings, M. Neel, K. Shaw
- BiologyEvolution; international journal of organic…
- 1 September 2008
It is demonstrated that the gsi provides a useful way to detect significant exclusivity even when groups are not monophyletic, and more broadly applicable to quantify and assess the significance of clustering of observations in labeled groups on any tree.
Comparing bootstrap and posterior probability values in the four-taxon case.
- M. P. Cummings, S. Handley, Daniel S. Myers, D. Reed, A. Rokas, K. Winka
- BiologySystematic Biology
- 1 August 2003
The results corroborate the findings of others that posterior probability values are excessively high and suggest that extrapolations from single topology branch-length studies are unlikely to provide any general conclusions regarding the relationship between bootstrap and posterior probabilities.
Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study
- J. C. Regier, A. Zwick, C. Mitter
- BiologyBMC Evolutionary Biology
- 2 December 2009
The results corroborate the broad outlines of the current working phylogenetic hypothesis for Ditrysia, demonstrate that some prominent features of that hypothesis, including the position of the butterflies, need revision, and resolve the majority of family and subfamily relationships within superfamilies as thus far sampled.
Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia.
- Shannon Takala-Harrison, Christopher G. Jacob, C. Plowe
- Biology, MedicineJournal of Infectious Diseases
- 1 March 2015
While there was some evidence of spreading resistance, there was no evidence of resistance moving westward from Cambodia into Myanmar, and K13 appears to be a major determinant of artemisinin resistance throughout Southeast Asia.
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