comparison hyphy_absrel.xml @ 6:f73435dc282b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"

5:bf204aabbf56

            <param name="log" value="false"/>
            <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive random effects branch-site model framework to test whether each branch has evolved under positive selection, using a procedure which infers an optimal number of rate categories per branch.

See the online documentation_ for more information.

.. _documentation: http://hyphy.org/methods/selection-methods/#absrel
    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msv022</citation>
    </expand>
</tool>

6:f73435dc282b

            <param name="log" value="false"/>
            <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
    
aBSREL : Adaptive Branch-Site Random Effects Likelihood
=======================================================  
    
What question does this method answer?
--------------------------------------

Is some proportion of sites is subject to positive selection along specific branches or lineages of a phylogeny?

Recommended Applications
------------------------

1. Exploratory testing for evidence of lineage-specific positive diversifying selection in small to medium sized alignments (up to 100 sequences).
2. Targeted testing of branches selected a priori for positive diversifying selection, including alignments with prohibitive runtimes under older branch-site models (up to 1,000 sequences) 

Brief description
-----------------

aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive
random effects branch-site model framework to test whether each branch
has evolved under positive selection, using a procedure which infers an
optimal number of rate categories per branch.


Input
-----

1. A *FASTA* sequence alignment.
2. A phylogenetic tree in the *Newick* format

Note: the names of sequences in the alignment must match the names of the sequences in the tree.


Output
------

A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).

For each tested branch the analysis will infer the appropriate number of selective regimes, 
and whether or not there is statistical evidence of positive selection on that branch.

A custom visualization module for viewing these results is available (see http://vision.hyphy.org/aBSREL for an example)

Further reading
---------------

http://hyphy.org/methods/selection-methods/#absrel


Tool options
------------
::


    --code              Which genetic code to use 

    --branches          Which branches should be tested for selection?
                            All [default] : test all branches
                            
                            Internal : test only internal branches (suitable for 
                            intra-host pathogen evolution for example, where terminal branches
                            may contain polymorphism data)
                            
                            Leaves: test only terminal (leaf) branches
                            
                            Unlabeled: if the Newick string is labeled using the {} notation,
                            test only branches without explicit labels 
                            (see http://hyphy.org/tutorials/phylotree/)

 

    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msv022</citation>
    </expand>
</tool>