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MODELTEST: testing the model of DNA substitution
SUMMARY The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. AVAILABILITY The MODELTEST package, including the source code and some
A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation.
TLDR
A strategy for estimating the set of cladograms that are consistent with a particular sample of either restriction site or nucleotide sequence data and that includes the possibility of recombination is presented.
GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes
TLDR
GeoDis is a computer program that implements the cladistic nested analysis in which population structure can be separated from population history when it is assessed through rigorous and objective statistical tests upon an estimated nested cladogram.
Evaluation of methods for detecting recombination from DNA sequences: Computer simulations
  • D. Posada, K. Crandall
  • Biology, Medicine
    Proceedings of the National Academy of Sciences…
  • 20 November 2001
TLDR
Methods that use substitution patterns or incompatibility among sites were more powerful than methods based on phylogenetic incongruence, and different recombination methods showed distinct performance depending on the amount of recombination, genetic diversity, and rate variation among sites.
TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees
The software program TreeSAAP measures the selective influences on 31 structural and biochemical amino acid properties during cladogenesis, and performs goodness-of-fit and categorical statistical
Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified
TLDR
It is demonstrated that the presence of COI numts makes this goal difficult to achieve when numts are prevalent and can introduce serious ambiguity into DNA barcoding, which strives for rapid and inexpensive generation of molecular species tags.
Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction.
TLDR
This work has shown that haplotype frequency in the sample contains information on the topological position of a given haplotype in a cladogram, which will allow one to reduce the number of alternative phylogenies and incorporate the uncertainties involved in reconstructing intraspecific phylogenies into subsequent analyses that depend heavily in the topology of the tree.
TCS: estimating gene genealogies
TLDR
The TCS algorithms are presented and initial attempts at parallelization are described and performance results are presented for the algorithm on several data sets.
Phylogeny Estimation and Hypothesis Testing Using Maximum Likelihood
One of the strengths of the maximum likelihood method of phylogenetic estimation is the ease with which hypotheses can be formulated and tested. Maximum likelihood analysis of DNA and amino acid
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