Loading...
  • NCBI
  • The idea is to use the tree for further analysis using R. Note that it is also possible for me to use ncbi taxa ids since i have them (not shown in this table). (biostars.org)
  • thanks Philipps, Do you know if is possible to change the name of the ncbi ids in the tree. (biostars.org)
  • Although i will use the ncbi taxids to recover the tree i would like to to change the taxid in the output tree with an OTU id. (biostars.org)
  • Alignment
  • NEW YORK (GenomeWeb News) - Researchers from the University of Texas at Austin have developed a new method - dubbed simultaneous alignment and tree estimation, or SATé - for estimating DNA alignment as a phylogenetic tree is constructed. (genomeweb.com)
  • A new non-alignment based approach, Relative Complexity Measure (RCM), has been introduced to tackle this problem and proven to work in fungi and mitochondrial DNA.Result: In this work, we present an application of the RCM method to reconstruct robust phylogenetic trees using sequence data for genus Galanthus obtained from different regions in Turkey. (biomedsearch.com)
  • From the alignment, we predict function of yet unannotated proteins, many of which we validate in the literature.The phylogenetic trees obtained in this way bear a striking resemblance to the ones obtained by sequence alignments.It does this independent of protein sequence or any other information external to network topology. (nih.gov)
  • 1000
  • The 26 virion RNA polymerase and large terminase subunits were compared using the ClustalW program, and the phylogenetic tree was generated with the neighbour-joining method and 1000 bootstrap replicates (CLC Genomics Workbench 6). (nih.gov)
  • Comparison of a sample of 1000 published trees with an essentially independent standard (dates of origin of groups in geological time) shows that the order of branching has improved slightly, but the disparity between estimated times of origination from phylogeny and stratigraphy has, if anything, become worse. (royalsocietypublishing.org)
  • The numbers at the branching points are the percentages of occurrence in 1000 bootstrapped trees. (nih.gov)
  • Phylip
  • When the run is done, right-click the "Download data in Newick/Phylip format" link to save the tree file as a text file on your harddisk (again make sure you can find it later). (dtu.dk)
  • This option is only useful when the tree is reconstructed using the mix program of phylip with the ancestral states specified in the file "ancestors" --nb-files number With this option, you specify the number of input files (1 and 2) to analyse This option only works for the association test. (ubuntu.com)
  • lengths
  • In a phylogenetic tree, each node with descendants represents the most recent common ancestor of the descendants, and edge lengths correspond to time estimates. (academickids.com)
  • A classical combinatorial result ensures that such trees can be uniquely reconstructed from the distances between the leaves (when the edges are given any strictly positive lengths). (springer.com)
  • Moreover, a linear number of these pairwise distance values suffices to determine both the tree and its edge lengths. (springer.com)
  • Also, we show that minimum triplet covers are 'shellable' and thereby provide a set of pairs for which the inter-leaf distance values will uniquely determine the underlying tree and its associated branch lengths. (springer.com)
  • This value of \(2n- 3\) cannot be made any smaller, since a binary unrooted tree with n leaves has \(2n-3\) edges, and the inter-leaf distances are linear combinations of the corresponding \(2n-3\) edge lengths (so, by linear algebra, these values cannot be uniquely determined by fewer than \(2n-3\) equations). (springer.com)
  • Also, we show that in that case the resulting triplet cover is 'shellable' which implies that the inter-leaf distances defined on these pairs uniquely determine the tree and its edge lengths. (springer.com)
  • experimental
  • Moreover, we show that split-specific measures are effective in determining which taxa or groups of taxa have low or high supports for an internal node, thus providing a valuable diagnostic tool to guide taxon sampling in experimental phylogenetic design. (mun.ca)
  • genetic
  • A) Comparison of the phylogenetic trees for protists obtained by genetic sequence alignments (left), H-GRAAL's metabolic network alignments (middle), and GRAAL's metabolic network alignments (right). (nih.gov)
  • taxa
  • Second, situating QTL data within a phylogenetic framework would directly account for the statistical dependencies that accompany any mapping comparison among three or more taxa. (genetics.org)
  • The mutant allele at the QTL could have arisen in one of five possible locations on the tree, and each location is associated with a particular partition of the four taxa into two groups (those with the "high" allele and those with the "low" allele). (genetics.org)
  • A branch in a phylogenetic tree and its associated internal node can be viewed as a split that separates the taxa into two nonempty subsets. (mun.ca)
  • branch
  • An algorithm was developed to project the node and branch structure of a tree into a multi-dimensional model [ 11 ]. (omicsonline.org)
  • Both our and GRAAL's tree differ from the sequence-based one in α single branch: Plasmodium falciparum (PFA) is misplaced in our tree, whereas Entamoeba histolytica (EHI) (or Dictyostelium discoideum (DDI)) is misplaced in GRAAL's tree. (nih.gov)
  • Classification
  • Trees with labelled leaves and with all other vertices of degree three play an important role in systematic biology and other areas of classification. (springer.com)
  • Trees play a central role in systematic biology, and other areas of classification, such as linguistics. (springer.com)
  • figure
  • The last figure above shows the unrooted tree. (dtu.dk)
  • To envision the problem, consider the tree in Figure 1 , and imagine the presence of a single diallelic QTL. (genetics.org)
  • Figure 1 shows the phylogenetic neighborhood of S. grandis str. (nih.gov)
  • viruses
  • Inspect the rooted tree that you get as a result of rerooting and consider what this tells you about the origin of HIV viruses. (dtu.dk)
  • amongst
  • These new functions provide the first means to directly transfer information amongst a wide range of phylogenetic trees and networks, as well as means to visualise and further analyse this information. (r-project.org)