Phylogenetic sequence data

Phylogenetic sequence data usually consist of multiple sequence alignments the individual, aligned-base positions are commonly referred to as sites. These sites are equivalent to characters in theoretical phylogenetic discussions, and the actual base (or gap) occupying a site is the character state. ... 

To date, only two exceptions to the pK of 8 rule have been found the Rieske protein from Sulfolobus acidocaldarius (139) and that from Thiobacillus ferrooxidans (140). In both cases, a first pK is observed in the vicinity of 6 (Fig. 7). The fact that Sulfolobus and Thiobacillus are phylogenetically almost as distant as they can possibly be, but share acidophilic growth conditions (medium-pH of 2), indicates that the pK, which is lower by 2 pH units in Sulfolobus and Thiobacillus, reflects adaptation. In the absence of structural information for the two acidophilic Rieske proteins, the molecular modifications resulting in this pK shift are difficult to guess. The absence of sequence data for the Thiobacillus protein furthermore precludes a comparative approach. It seems likely, however, that the solvent-exposed histidine ligands to the cluster will become slightly more bur-... 

Hibsch-Jetter, C. 2001. Phylogenetic relationships in Chrysosplenium (Saxifragaceae) based on analysis of a combined rbcUmatK sequence data set. Amer. J. Bot. 88 883-893. 

Chilton, N.B., Gasser, R.B. and Beveridge, I. (1997a) Phylogenetic relationships of Australian strongyloid nematodes inferred from ribosomal DNA sequence data. InternationalJournal for Parasitology 27,1481-1494. 

Some authors concentrate mainly on phylogenetic aspects based on sequence data. The amino acid sequences of a considerable number of well-studied transporters from many bacteria are published, and an immense set of primary sequence data will become available within the next few years (primarily from numerous genome projects). Phylogenetic trees of transport proteins are... 

Choi, H.-K., and Wen, J. (2000). A phylogenetic analysis of Panax (Araliaceae) Integrating cpDNA restriction site and nuclear rDNA ITS sequence data. Plant Syst. Evol. 224, 109-120. 

Bishit and Mukai (2000,2001 a,b), in a series of FISH (fluorescent in situ hybridization) studies, reported that there were three diploid species. The two tetraploid species . africana and . coracana are related to one another. They also suggested that . multiflora was a distinct species and that the two diploid species . indica and . floccifolia are probably the donors to the tetraploid species. This conclusion was based on the pattern of hybridization of a 5sRNA probe of the chromosomes of the species that they studied. However, phylogenetic analysis of sequence data does not appear to support this hypothesis none of the ITS found in E. coracana closely related to the ITS of E. floccifolia (Neves et al. 2005). 

Roodt-Wilding, R. and Spies, J. J. (2006). Phylogenetic relationships in southern African chloridoid grasses (Poaceae) based on nuclear and chloroplast sequence data. System. 

Sequence data can be analyzed for (a) Sequence characteristics by knowledge-based sequence analysis, (b) Similarity search by pairwise sequence comparison, (c) Multiple sequence alignment, (d) Sequence motif discovery in multiple alignment, and (e) phylogenetic inference. 

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. 

Arisue N, Hashimoto T, Yoshikawa H, Nakamura Y, Nakamura G, Nakamura F, Yano TA, Hasegawa M (2002c) Phylogenetic position of Blastocystis hominis and of stramenopiles inferred from multiple molecular sequence data. J Eukaryot Microbiol 49 42-53... 

Procedures involved in the analysis of rRNA sequence data for inferring phylogenetic relationships have been extensively discussed.24,25 A critical prerequisite is that sequence alignments be carefully examined by reference to rRNA secondary structure.23,26... 

Fig. I. Flowchart of steps from obtaining the sequence data to assessing the reliability of the final phylogenetic result.

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