View source for Gblocks

[[Category:Software]][[Category:Biology]]
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Gblocks is a computer program written in ANSI C language that eliminates
poorly aligned positions and divergent regions of an alignment of DNA or
protein sequences. These positions may not be homologous or may have been
saturated by multiple substitutions and it is convenient to eliminate them
prior to phylogenetic analysis. Gblocks selects blocks in a similar way as
it is usually done by hand but following a reproducible set of conditions.
The selected blocks must fulfill certain requirements with respect to the
lack of large segments of contiguous nonconserved positions, lack or low
density of gap positions and high conservation of flanking positions, making
the final alignment more suitable for phylogenetic analysis. Gblocks outputs
several files to visualize the selected blocks. The use of a program such as
Gblocks reduces the necessity of manually editing multiple alignments, makes
the automation of phylogenetic analysis of large data sets feasible and,
finally, facilitates the reproduction of the alignments and subsequent
phylogenetic analysis by other researchers.

Several parameters can be modified to make the selection of blocks more or
less stringent. In general, a relaxed selection of blocks is better for
short alignments, whereas a stringent selection is more adequate for longer
ones. Be aware that the default options of Gblocks are stringent.

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