Mercurial > repos > iuc > hyphy_sm19
diff hyphy_sm19.xml @ 5:5f1830cb9135 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
author | iuc |
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date | Thu, 20 Feb 2020 18:09:55 -0500 |
parents | ae7c42d49717 |
children | 638942ba8e37 |
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--- a/hyphy_sm19.xml Mon Feb 17 14:53:22 2020 -0500 +++ b/hyphy_sm19.xml Thu Feb 20 18:09:55 2020 -0500 @@ -63,15 +63,76 @@ </test> </tests> <help><![CDATA[ -This analysis implements canonical and modified versions of the Slatkin-Maddison -phylogeny based test for population segregation. The test estimates the minimum -number of migration events using maximum parsimony, and then evaluating whether -or not this number is lower than expected in a panmictic or unstructured -population using permutation tests. + +SM2019 : Structured Slatkin-Maddison +==================================== + +What does this do? +------------------ + +Test for evidence of genetically segregated populations, using a "detuned" version of +the Slatkin-Maddison test. + +Brief description +----------------- + +This analysis implements canonical and modified versions of the +Slatkin-Maddison phylogeny based test for population segregation. The +test estimates the minimum number of migration events using maximum +parsimony, and then evaluating whether or not this number is lower than +expected in a panmictic or unstructured population using permutation +tests + +Input +----- + +1. A phylogenetic tree in the *Newick* format + +Note: assumes that leaf names that can be partitioned into sets using regular expressions + +For example + +:: + + ((((((((x_US_x_A_01C:0.0125396,(((((x_US_x_A_01P:0.00887628,(( + x_US_x_A_08P:-0.000190918,x_US_x_A_11P:0.00313157):0.0106883, + x_US_x_A_14C:0.0103815):0.00311658):0.00120812,x_US_x_A_09P:0.00320468): + 0.0108828,x_US_x_A_12P:0.00732672):0.00596663,x_US_x_A_07C:0.00449846):0 + .00639319,((((x_US_x_A_02P:-2.62303e-05,x_US_x_A_05P:0.00591507):0. + 000156788,x_US_x_A_04P:0.00576826):0.00907366,((x_US_x_A_03P:0.00941548, + x_US_x_A_14P:0.00866127):0.00229499,x_US_x_A_13P:0.0209192):0.00469629): + 0.0146758,(x_US_x_A_10P:0.000156443,x_US_x_A_15P:0.00578946):0.00472532) + :0.0103079):0.00733948):0.00228489,x_US_x_A_06P:0.00557974):0.00472981, + x_US_x_A_04C:0.00478858):0.00105548,x_US_x_A_05C:0.0120259):0.0060905, + x_US_x_A_12C:0.002911):2.90824e-05,x_US_x_A_11C:-5.79432e-06):4.34574e- + 06,x_US_x_A_13C:-4.34574e-06):4.34574e-06,((x_US_x_A_08C:0.0029538, + x_US_x_A_09C:-1.31511e-05):0.00296627,x_US_x_A_10C:-8.69148e-06):4. + 34574e-06,x_US_x_A_15C:-4.34574e-06); + +Which can be partitioned into two groups of leaves, those that end in "P", and those that +end in "C" + +1. Reg-exp 1: `P^` +2. Reg-exp 2: `C^` + + +Output +------ + +A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). + +A custom visualization module for viewing these results is available (see http://vision.hyphy.org/Slatkin for an example) + +Further reading +--------------- + +https://github.com/veg/hyphy-analyses/tree/master/SlatkinMaddison + + ]]></help> <expand macro="citations"> <citation type="bibtex"> - @UNPUBLISHED{slatkin, + @PUBLISHED{slatkin, author = "Slatkin M, Maddison WP", title = "A cladistic measure of gene flow inferred from the phylogenies of alleles", year = "1989",