Jackknife and Bootstrap Tests of the Composition Vector Trees

Composition vector trees （CVTrees） are inferred from whole-genome data by an alignment-free and parameter-free method. The agreement of these trees with the corresponding taxonomy provides an objective justification of the inferred phylogeny. In this work, we show the stability and self-consistency of CVTrees by performing bootstrap and jackknife re-sampling tests adapted to this alignment-free approach. Our ultimate goal is to advocate the viewpoint that time-consuming statistical re-sampling tests can be avoided at all in using this alignment-free approach. Agreement with taxonomy should be taken as a major criterion to estimate prokaryotic phylogenetic trees.

Prokaryote phylogeny meets taxonomy: An exhaustive comparison of composition vector trees with systematic bacteriology

We perform an exhaustive, taxon by taxon, comparison of the branchings in the composition vector trees (CVTrees) inferred from 432 prokaryotic genomes available on 31 December 2006, with the bacte-riologists' taxonomy-primarily the latest online Outline of the Bergey's Manual of Systematic Bacteri-ology. The CVTree phylogeny agrees very well with the Bergey's taxonomy in majority of fine branchings and overall structures. At the same time most of the differences between the trees and the Manual have been known to biologists to some extent and may hint at taxonomic revisions. Instead of demonstrating the overwhelming agreement this paper puts emphasis on the biological implications of the differences.

CVTree: A Parallel Alignment-free Phylogeny and Taxonomy Tool Based on Composition Vectors of Genomes

Composition Vector Tree(CVTree) is an alignment-free algorithm to infer phylogenetic relationships from genome sequences. It has been successfully applied to study phylogeny and taxonomy of viruses, prokaryotes, and fungi based on the whole genomes, as well as chloroplast genomes, mitochondrial genomes, and metagenomes. Here we presented the standalone software for the CVTree algorithm. In the software, an extensible parallel workflow for the CVTree algorithm was designed. Based on the workflow, new alignment-free methods were also implemented. And by examining the phylogeny and taxonomy of 13,903 prokaryotes based on 16 S r RNA sequences, we showed that CVTree software is an efficient and effective tool for studying phylogeny and taxonomy based on genome sequences. The code of CVTree software can be available at https://github.com/ghzuo/cvtree.

High-rise building fire pre-warning model based on the support vector regression

Aiming at reducing the deficiency of the traditional fire pre-warning algorithms and the intelligent fire pre-warning algorithms such as artificial neural network,and then to improve the accuracy of fire prewarning for high-rise buildings,a composite fire pre-warning controller is designed according to the characteristic（ nonlinear,less historical data,many influence factors）,also a high-rise building fire pre-warning model is set up based on the support vector regression（ SV R）. Then the wood fire standard history data is applied to make empirical analysis. The research results can provide a reliable decision support framework for high-rise building fire pre-warning.

Shigella Strains Are Not Clones of Escherichia coli but Sister Species in the Genus Escherichia

Shigella species and Escherichia coli are closely related organisms. Early phenotyping experiments and several recent molecular studies put Shigella within the species E. coli. However, the whole-genome-based, alignment-free and parameter-free CVTree approach shows convincingly that four established Shigella species, Shigella boydii, Shigella sonnei, Shigella felxneri and Shigella dysenteriae, are distinct from E. coli strains, and form sister species to E. coli within the genus Esch- erichia. In view of the overall success and high resolution power of the CVTree approach, this result should be taken seriously. We hope that the present report may promote further in-depth study of the Shigella-E. coli relationship.

CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy

A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http：//tlife.fudan.edu.cn/cvtree3/without login requirements.

On monospecific genera in prokaryotic taxonomy

A monospecific genus contains a single species ever since it was proposed.Though formally more than half of the known prokaryotic genera are monospecific,we pick up those which actually raise taxonomic problems by violating monophyly of the taxon within which it resides.Taking monophyly as a guiding principle,our arguments are based on simultaneous support from 16S rRNA sequence analysis and whole-genome phylogeny of prokaryotes,as provided by the LVTree Viewer and CVTree Web Server,respectively.The main purpose of this study consists in calling attention to this specific way of global taxonomic analysis.Therefore,we refrain from making formal emendations for the time being.