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MODELTEST: testing the model of DNA substitution
TLDR
MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. Expand
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TCS: a computer program to estimate gene genealogies
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A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation.
We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypicExpand
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GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes
The central focus of population genetics is the study of the distribution of the genetic variation within and among populations. This endeavour has often been accomplished by the use of genealogiesExpand
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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
Recombination is a key evolutionary process that shapes the architecture of genomes and the genetic structure of populations. Although many statistical methods are available for the detection ofExpand
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Selecting the best-fit model of nucleotide substitution.
Despite the relevant role of models of nucleotide substitution in phylogenetics, choosing among different models remains a problem. Several statistical methods for selecting the model that best fitsExpand
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A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints.
We have developed a modified BOOTSCAN algorithm that may be used to screen nucleotide sequence alignments for evidence of recombination without prior identification of nonrecombinant referenceExpand
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TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees
TLDR
TreeSAAP measures the selective influences on 31 structural and biochemical amino acid properties during cladogenesis, and performs goodness-of-fit and categorical statistical tests. Expand
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Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified
Nuclear mitochondrial pseudogenes (numts) are nonfunctional copies of mtDNA in the nucleus that have been found in major clades of eukaryotic organisms. They can be easily coamplified withExpand
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Multiple and ancient origins of the domestic dog.
Mitochondrial DNA control region sequences were analyzed from 162 wolves at 27 localities worldwide and from 140 domestic dogs representing 67 breeds. Sequences from both dogs and wolves showedExpand
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