Software phylogenetic analysis

DDBJ EBI List of phylogenetic analysis software http //www.ddbj.nig.ac.jp/ http //www2.ebi.ac.uk/clastalw/ http //evolution.gentics.washington.edu/philip/software.html... 

PHYLIP and PAUP compete as the most widely used phylogenetic analysis software, although other newer applications such as PUZZLE are begiiming to compete. Here, PHYLIP and PAUP will be described in the most detail, with references made to other available packages that have useful features. However, the number of programs available is now so numerous, many each having their own useful features, that the... 

Phylogenetic analysis software programs Phylogeny databases and utilities ... 

Phylogenetic analysis is the means of inferring or estimating evolutionary relationships. Nucleotide sequences of DNA or RNA and amino acid sequences of proteins are the most popular data used to construct phylogenetic trees. Methods of phylogenetic analysis using sequence data are introduced and performed with a software package, PHYLIP locally and online. 

Phylip (Phylogenetic Inference Package) is a software package comprising about 30 command-line programs that cover almost any aspect of phylogenetic analysis... 

TABLE 18.4 Some software programs for phylogenetic analysis of biosequences... 

ToolBus comprises several data analysis software platforms such as multiple sequence alignment, phylogenetic trees, generic XML viewer, pathways, and microarray analysis, which are linked to each other as well as to major databases. SRS and NCBI serve as general data retrieval portals as well as provide links to specific analysis tools. 

There are numerous computer software programs that permit one to investigate sequence ahgnment and phylogenetic relationships among (a) various proteins, domains, motifs, modules, etc., and (b) nucleic acid sequences in DNA and RNA. In addition to those presented below, various Internet-based algorithms afford rapid and convenient analysis of macromolecular sequences. 

Comparative sequence analysis and ERNA-3D software were used to model the three-dimensional structures of several signal recognition particle RNAs. RNA secondary structures were established by allowing only phylogenetically-supported base pairs. The folding of the RNA molecules was constrained further to include a pseudoknot and a tertiary interaction. Founded by the concept that all SRP RNAs must be shaped similarly in three dimensions, helical sections were oriented coaxially where a continuous helical stack was formed in the RNA of another species. Finally, RNA helices were placed at distances that preserved the connectivity of the molecule with the smallest number of single-stranded nucleotide residues as identified from the aligned sequences. Representative models of the three-dimensional structures of an eukaryote, an archaeon, and three bacterial SRP RNAs are presented. 

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