Old phylogenies

The old version of ZARAMIT was aimed to develop working system prototypes capable of automating every step in the reconstruction process and building exhaustive, statistically supported phylogenies over very large datasets. Particular attention was paid to human mitochondrial DNA as a fertile ground for development and experimentation in both biological and computational matters. We built 5 phylogenies:

  1. 5000-sequence human mitochondrial phylogeny (August 2008) [tree]
    Distance matrix (default F84 model) + neighbor joining + 100-sample bootstrap. Rooted with the chimpanzee reference sequence. [info]
  2. 5320-sequence human mitochondrial phylogeny (February 2009) [tree]
    Distance matrix (adjusted F84 model) + neighbor joining + 100-sample bootstrap. The model of evolution uses a transition/transversion ratio of 60, and gamma-distributed rates across sites (α ≈ 0.5). Rooted with the chimpanzee reference sequence. [info]
  3. 5614-sequence human mitochondrial phylogeny (March 2009) [tree]
    Distance matrix (adjusted F84 model, see above) + neighbor joining + 100-sample bootstrap. Rooted with the chimpanzee reference sequence. [info]
  4. X4895-sequence human mitochondrial phylogeny (October 2009) [tree] [leaves] [ancestors]
    Distance matrix (adjusted F84 model, see above) + neighbor joining + 200-sample bootstrap. Extensive, curated phylogeny. [info]
  5. X7390-sequence human mitochondrial phylogeny (February 2011) [tree] [leaves] [ancestors]
    Maximum likelihood (GTR+Γ model) + 200-sample bootstrap. Extensive, curated phylogeny. The model employs GTRCAT approximation and is optimized automatically for each sample. Rooted with H. neanderthalensis and H. sp. altai sequences. [info]