Phylogenomics - a "how to" overview



A phylogenetic tree is constructed in the following basic steps:

Several computer programs are available for database searches. Multiple searches using different programs should be performed, since the programs differ in their sensitivity (1). A good alignment is a prerequisite for a meaningful phylogenetic tree. At this step it is also important, to use more than one program to obtain an optimal alignment (2). There are also different methods and programs for construction of phylogenetic trees, which can vary significantly in computational speed. The phylogenetic trees obtained by the different combinations of methods are usually stored in database in different formats (machine readable, image).
However, the interplay between the different applications is automated only in special instances (3, 4). For large scale phylogenomic studies, it will be absolutely necessary to streamline the whole process. Furthermore, due to the rapid increase of available genome sequences, the generation of phylogenetic trees should be repeated in appropriate time intervals in order to update the tree databases.
It should be also noted that the currently available tree building algorithms are not optimized for inferring phylogenetic relationships. However, reasonably good results are obtained using the currently available programs. Nevertheless, development of novel algorithms, optimized for the phylogenomics approach, is highly desirable.
    (1) Brenner, S.E., Chotia, C., and Hubbard, T.J.P. 1998. Proc. Natl. Acad. Sci. 95: 6073-6078.
    (2)Thompson, J.D., Plewniak, F., and Poch, O. 1999. Nucleic Acids Res. 27: 2682-2690.
    (3) Sicheritz-Pontén, T., and Andersson, S.G.E. 2001. Nucleic Acids Res. 29: 545-552.
    (4) Zmasek, C.M., and Eddy, S.R. 2001. Bioinformatics 17: 821-828.

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