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