Details
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Type:
New Feature
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Status: Closed
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Priority:
Minor
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Resolution: Won't Fix
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Affects Version/s: 1.0
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Fix Version/s: None
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Component/s: jaba-cli
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Labels:
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Environment:Gblocks provides binaries for the following Mac OS X / Universal , Windows, Linux / x86, Linux 64, UNIX OSF1 / Alpha, UNIX IRIX64 / SGI, UNIX SunOS / SPARC
Description
Gblocks Download: http://molevol.cmima.csic.es/castresana/Gblocks.html
Documentation: http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_documentation.html
Gblocks is an essential tool for building phylogenies from problematic alignments. It allows you to select conserved contiguous regions from your aligned protein that would otherwise require manual editing of the alignment, which is a rather subjective activity and not particularly reproducible. Several papers have shown this improves the phylogeny 'signal'.
Practically Gblocks works just like an alignment program, in that it accepts FASTA or MSF files and returns a alignment in the same format. The major difference is that it will not tolerate alignments with sequences of different lengths. One possible way to deal with this is to append gaps or unknown bases to make the sequences the same length, or simply to trim all sequences to the same length.
Documentation: http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_documentation.html
Gblocks is an essential tool for building phylogenies from problematic alignments. It allows you to select conserved contiguous regions from your aligned protein that would otherwise require manual editing of the alignment, which is a rather subjective activity and not particularly reproducible. Several papers have shown this improves the phylogeny 'signal'.
Practically Gblocks works just like an alignment program, in that it accepts FASTA or MSF files and returns a alignment in the same format. The major difference is that it will not tolerate alignments with sequences of different lengths. One possible way to deal with this is to append gaps or unknown bases to make the sequences the same length, or simply to trim all sequences to the same length.