comparison alignment/gblocks.xml @ 0:5b9a38ec4a39 draft default tip

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0:5b9a38ec4a39

<tool id="gblocks" name="Gblocks" version="1.0">
    <description>Convert Aligned FASTA to phylip Extended</description>
    <command interpreter="perl">
        gblocks.pl $input $datatype $gaps $Block $out_file $html_file > $screen
    </command>
    <inputs>
            <param name="input" type="data" format="fasta" label="Input Fasta File" help="Aligned fasta" />
    <param name="datatype" type="select" label="Type of Sequence">
      <option value="-t=d">DNA</option>
      <option value="-t=p">Protein</option>
      <option value="-t=c">Codons</option>
    </param>
    <param name="Block" type="integer" value="10" label="Minimum block size" help='10 is default. Smaller values less stringent.'/>
    <param name="gaps" type="select" label="Gap Allowance">
      <option value="-b5=n">None</option>
      <option value="-b5=h">Half</option>
      <option value="-b5=a">All</option>
    </param>
    </inputs>
    <outputs>
        <data format="txt" name="screen" label="${tool.name} on ${on_string}: screen Log" />
        <data format="html" name="html_file" label="${tool.name} on ${on_string}: html File"/>
        <data format="txt" name="out_file" label="${tool.name} on ${on_string}: Output File"/>
    </outputs>
    <help>
**What it does**

About GBlocks

Version 0.91b, January 2002

Copyright Jose Castresana

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 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. Gblocks is very fast in processing alignments and it is therefore highly 
suitable for large-scale phylogenetic analyses.

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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**Inputs**

FASTA

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**Outputs**

Phylip extended

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**Additional Information**

Please direct questions or comments to [e-mail] or, if you can, enter them on the osiris_phylogenetics site at
bitbucket.org

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**Citations**

This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider
citing the following.

Current Osiris Citation is here

http://osiris-phylogenetics.blogspot.com/2012/10/citation.html

Additional Citations for this tool

Talavera, G., and Castresana, J. (2007). Improvement of phylogenies after removing 
divergent and ambiguously aligned blocks from protein sequence alignments. Systematic 
Biology 56, 564-577.

Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their 
use in phylogenetic analysis. Molecular Biology and Evolution 17, 540-552.
    </help>
</tool>