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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 <tool id="gblocks" name="Gblocks" version="1.0">
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 <description>Convert Aligned FASTA to phylip Extended</description>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 <command interpreter="perl">
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4 gblocks.pl $input $datatype $gaps $Block $out_file $html_file > $screen
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5 </command>
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6 <inputs>
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7 <param name="input" type="data" format="fasta" label="Input Fasta File" help="Aligned fasta" />
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 <param name="datatype" type="select" label="Type of Sequence">
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9 <option value="-t=d">DNA</option>
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10 <option value="-t=p">Protein</option>
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11 <option value="-t=c">Codons</option>
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12 </param>
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13 <param name="Block" type="integer" value="10" label="Minimum block size" help='10 is default. Smaller values less stringent.'/>
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14 <param name="gaps" type="select" label="Gap Allowance">
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15 <option value="-b5=n">None</option>
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16 <option value="-b5=h">Half</option>
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17 <option value="-b5=a">All</option>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data format="txt" name="screen" label="${tool.name} on ${on_string}: screen Log" />
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22 <data format="html" name="html_file" label="${tool.name} on ${on_string}: html File"/>
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23 <data format="txt" name="out_file" label="${tool.name} on ${on_string}: Output File"/>
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24 </outputs>
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25 <help>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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26 **What it does**
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27
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 About GBlocks
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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29
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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30 Version 0.91b, January 2002
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31
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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32 Copyright Jose Castresana
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33
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34 Gblocks is a computer program written in ANSI C language that eliminates poorly aligned
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35 positions and divergent regions of an alignment of DNA or protein sequences. These
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36 positions may not be homologous or may have been saturated by multiple substitutions and it
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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37 is convenient to eliminate them prior to phylogenetic analysis. Gblocks selects blocks in a
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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38 similar way as it is usually done by hand but following a reproducible set of conditions.
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39 The selected blocks must fulfill certain requirements with respect to the lack of large
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40 segments of contiguous nonconserved positions, lack of gap positions and high conservation
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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41 of flanking positions, making the final alignment more suitable for phylogenetic analysis.
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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42 Gblocks outputs several files to visualize the selected blocks. The use of a program such
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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43 as Gblocks reduces the necessity of manually editing multiple alignments, makes the
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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44 automation of phylogenetic analysis of large data sets feasible and, finally, facilitates
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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45 the reproduction of the alignments and subsequent phylogenetic analysis by other
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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46 researchers. Gblocks is very fast in processing alignments and it is therefore highly
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47 suitable for large-scale phylogenetic analyses.
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48
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49 Several parameters can be modified to make the selection of blocks more or less stringent.
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50 In general, a relaxed selection of blocks is better for short alignments, whereas a
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51 stringent selection is more adequate for longer ones. Be aware that the default options of
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52 Gblocks are stringent.
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53
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54 ------
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55
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56 **Inputs**
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57
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58 FASTA
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59
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60 ------
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61
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62 **Outputs**
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63
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64 Phylip extended
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65
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66 -------
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67
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68 **Additional Information**
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69
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70 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at
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71 bitbucket.org
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72
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73 -------
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74
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75 **Citations**
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76
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77 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
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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78 citing the following.
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79
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80 Current Osiris Citation is here
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81
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82 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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83
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84 Additional Citations for this tool
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85
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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86 Talavera, G., and Castresana, J. (2007). Improvement of phylogenies after removing
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87 divergent and ambiguously aligned blocks from protein sequence alignments. Systematic
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88 Biology 56, 564-577.
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89
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90 Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their
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91 use in phylogenetic analysis. Molecular Biology and Evolution 17, 540-552.
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92 </help>
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93 </tool>