comparison assembly_post_processor.xml @ 31:0fad708a9693 draft

Uploaded

30:0d680d17278c

 * **Protein clustering method** - gene family scaffold protein clustering method.  Each PlantTribes scaffold data has up to three sets of clusters - GFam[8] (clusters of consensus domain architecture), OrthoFinder[9] (broadly defined clusters) or OrthoMCL[10] (narrowly defined clusters).  You can also install your own data scaffold created using a different clustering method as long as it conforms to the PlantTribes scaffold data format.
 * **Trim alignments** - trim gene family multiple sequence alignments that include scaffold backbone genes and locally assembled transcripts to remove non-conserved regions (gappy sites)[11].  The trimmed alignments are used in assigning scores to locally assembled transcripts to determine how well they compare to the backbones gene models.  The default setting of 0.1 removes sites tha thave gaps in 90% of the sequences in the multiple sequence alignment.  This option is restricted to the range 0.0 - 1.0.
 * **Strand-specific assembly?** - select 'Yes' if transcriptome library sequences were strand-specific.  If 'Yes" is selected, transcripts from the minority strand (antisense) are removed.
 * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12].
 * **Minimum sequence length** - set the minimum sequence length of predicted coding regions. The default is 200 bp.
 
    </help>
    <citations>
        <citation type="bibtex">
            @article{None,
            journal = {None},

            year = {2013},
            url = {http://hmmer.org},}
        </citation>
    </citations>
</tool>

31:0fad708a9693

 * **Protein clustering method** - gene family scaffold protein clustering method.  Each PlantTribes scaffold data has up to three sets of clusters - GFam[8] (clusters of consensus domain architecture), OrthoFinder[9] (broadly defined clusters) or OrthoMCL[10] (narrowly defined clusters).  You can also install your own data scaffold created using a different clustering method as long as it conforms to the PlantTribes scaffold data format.
 * **Trim alignments** - trim gene family multiple sequence alignments that include scaffold backbone genes and locally assembled transcripts to remove non-conserved regions (gappy sites)[11].  The trimmed alignments are used in assigning scores to locally assembled transcripts to determine how well they compare to the backbones gene models.  The default setting of 0.1 removes sites tha thave gaps in 90% of the sequences in the multiple sequence alignment.  This option is restricted to the range 0.0 - 1.0.
 * **Strand-specific assembly?** - select 'Yes' if transcriptome library sequences were strand-specific.  If 'Yes" is selected, transcripts from the minority strand (antisense) are removed.
 * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12].
 * **Minimum sequence length** - set the minimum sequence length of predicted coding regions. The default is 200 bp.

    </help>
    <citations>
        <citation type="bibtex">
            @article{None,
            journal = {None},

            year = {2013},
            url = {http://hmmer.org},}
        </citation>
    </citations>
</tool>