• Publications
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Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
  • J. Castresana
  • Biology, Medicine
  • Molecular biology and evolution
  • 1 April 2000
TLDR
A computerized method is presented that reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers. Expand
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.
TLDR
Whether phylogenetic reconstruction improves after alignment cleaning or not is examined and cleaned alignments produce better topologies although, paradoxically, with lower bootstrap, which indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies. Expand
Phylogenetic and Ecological Analysis of Novel Marine Stramenopiles
TLDR
A comparative analysis of novel stramenopiles is carried out, including new sequences from coastal genetic libraries presented here and sequences from recent reports from the open ocean and marine anoxic sites, confirming that they are fundamental members of the marine eukaryotic picoplankton. Expand
The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees
TLDR
A new phylogenetic comparison method that measures overall differences in the relative branch length and topology of two phylogenetic trees, resulting in the minimum branch length distance or K tree score, which allows the evaluation of the performance of phylogenetic algorithms, not only with respect to their topological accuracy, but also to the reproduction of a given branch length variation. Expand
Cytochrome b phylogeny and the taxonomy of great apes and mammals.
  • J. Castresana
  • Biology, Medicine
  • Molecular biology and evolution
  • 1 April 2001
TLDR
Using maximum-likelihood phylogenetic trees constructed from a large number of complete or nearly complete mammalian cytochrome b sequences, it is shown that the distributions of intrageneric and intergeneric distances derived from these trees are clearly separated, which allows the limits for a more rational generic classification of mammals to be established. Expand
Inverse relationship between evolutionary rate and age of mammalian genes.
TLDR
It is shown that older genes tend to evolve more slowly than newer ones; that is, proteins that arose earlier in evolution currently have a larger proportion of sites subjected to negative selection. Expand
Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen.
TLDR
It is proposed that aerobic metabolism in organisms with cytochrome oxidase has a monophyletic and ancient origin, prior to the appearance of eubacterial oxygenic photosynthetic organisms. Expand
Cytochrome oxidase evolved by tinkering with denitrification enzymes
The cytochrome bc complex which is encoded by the fixNOPQ operon in Bradyrhizobiumjaponicum, is the most distant member of the haem‐copper cytochrome oxidase family. We have found that its majorExpand
Nitric oxide reductases in bacteria.
TLDR
The current knowledge on bacterial NORs is summarized, the evolutionary relationship between them and cytochrome oxidases is discussed, and two types ofacterial NORs have been characterised. Expand
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