comparison phylogenomics_analysis.xml @ 70:bd26a18387ae draft

Uploaded

69:34dcfb570551

<tool id="plant_tribes_phylogenomics_analysis" name="Create multiple sequence alignments" version="0.6.0">
    <description>and inferred maximum likelihood phylogenies</description>
    <requirements>
        <requirement type="package" version="0.6">plant_tribes_phylogenomics_analysis</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->

  - **Remove sites in alignments with gaps of** - If the process used for gap trimming is nucleotide based, this is the gap value used when removing gappy sites in alignments (i.e., 0.1 removes sites with 90% gaps).

    </help>
    <citations>
        <citation type="bibtex">
            @unpublished{None,
            author = {Eric Wafula},
            title = {None},
            year = {None},
            url = {https://github.com/dePamphilis/PlantTribes}
            }
        </citation>
        <citation type="doi">10.1093/bioinformatics/btw412</citation>
        <citation type="bibtex">
            @published{Research in Computational Molecular Biology (RECOMB) (pp. 177–191),
            author = {Mirarab, S., Nguyen, N., Warnow, T.},
            title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan
            (Ed.)},
            year = {2014},
            url = {https://github.com/smirarab/pasta}
            }
        </citation>
        <citation type="bibtex">
            @published{Bioinformatics,
            author = {Salvador Capella-Gutierrez, Jose M. Silla-Martinez, Toni
            Gabaldon},
            title = {trimAl: a tool for automated alignment trimming in large-scale
            phylogenetic analyses},
            year = {2009},
            url = {http://trimal.cgenomics.org}
            }
        </citation>
        <citation type="bibtex">
            @published{Bioinformatics,
            author = {A. Stamatakis},
            title = {RAxML Version 8: A tool for Phylogenetic Analysis and
            Post-Analysis of Large Phylogenies},
            year = {2014},
            url = {http://sco.h-its.org/exelixis/web/software/raxml/index.html}
            }
        </citation>
        <citation type="doi">10.1371/journal.pone.0009490</citation>
    </citations>
</tool>

70:bd26a18387ae

<tool id="plant_tribes_phylogenomics_analysis" name="PhylogenomicsAnalysis" version="0.6.0">
    <description>builds gene family multiple sequence alignments and their corresponding phylogenies</description>
    <requirements>
        <requirement type="package" version="0.6">plant_tribes_phylogenomics_analysis</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->

  - **Remove sites in alignments with gaps of** - If the process used for gap trimming is nucleotide based, this is the gap value used when removing gappy sites in alignments (i.e., 0.1 removes sites with 90% gaps).

    </help>
    <citations>
        <citation type="bibtex">
            @misc{None,
            journal = {None},
            author = {1. Wafula EK},
            title = {Manuscript in preparation},
            year = {None},
            url = {https://github.com/dePamphilis/PlantTribes},}
        </citation>
        <citation type="bibtex">
            @article{Mirarab2014,
            journal = {Research in Computational Molecular Biology (RECOMB)},
            author = {2. Mirarab S, Nguyen N, Warnow T},
            title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan (Ed.)},
            year = {2014},
            pages = {177–191},
            url = {https://github.com/smirarab/pasta},}
        </citation>
        <citation type="bibtex">
            @article{Salvador2009,
            journal = {Bioinformatics},
            author = {3. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T},
            title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
            year = {2009},
            url = {http://trimal.cgenomics.org},}
        </citation>
        <citation type="bibtex">
            @article{Stamatakis2014,
            journal = {Bioinformatics},
            author = {4. Stamatakis A},
            title = {RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies},
            year = {2014},
            url = {http://sco.h-its.org/exelixis/web/software/raxml/index.html},}
        </citation>
        <citation type="doi">10.1371/journal.pone.0009490</citation>
        <citation type="doi">10.1093/bioinformatics/btw412</citation>
    </citations>
</tool>