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comparison hyphy_sm19.xml @ 5:5f1830cb9135 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
author iuc
date Thu, 20 Feb 2020 18:09:55 -0500
parents ae7c42d49717
children 638942ba8e37
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4:c60fcdf8f01e 5:5f1830cb9135
61 </repeat> 61 </repeat>
62 <output name="sm19_output" file="sm19-out2.json" compare="sim_size"/> 62 <output name="sm19_output" file="sm19-out2.json" compare="sim_size"/>
63 </test> 63 </test>
64 </tests> 64 </tests>
65 <help><![CDATA[ 65 <help><![CDATA[
66 This analysis implements canonical and modified versions of the Slatkin-Maddison 66
67 phylogeny based test for population segregation. The test estimates the minimum 67 SM2019 : Structured Slatkin-Maddison
68 number of migration events using maximum parsimony, and then evaluating whether 68 ====================================
69 or not this number is lower than expected in a panmictic or unstructured 69
70 population using permutation tests. 70 What does this do?
71 ------------------
72
73 Test for evidence of genetically segregated populations, using a "detuned" version of
74 the Slatkin-Maddison test.
75
76 Brief description
77 -----------------
78
79 This analysis implements canonical and modified versions of the
80 Slatkin-Maddison phylogeny based test for population segregation. The
81 test estimates the minimum number of migration events using maximum
82 parsimony, and then evaluating whether or not this number is lower than
83 expected in a panmictic or unstructured population using permutation
84 tests
85
86 Input
87 -----
88
89 1. A phylogenetic tree in the *Newick* format
90
91 Note: assumes that leaf names that can be partitioned into sets using regular expressions
92
93 For example
94
95 ::
96
97 ((((((((x_US_x_A_01C:0.0125396,(((((x_US_x_A_01P:0.00887628,((
98 x_US_x_A_08P:-0.000190918,x_US_x_A_11P:0.00313157):0.0106883,
99 x_US_x_A_14C:0.0103815):0.00311658):0.00120812,x_US_x_A_09P:0.00320468):
100 0.0108828,x_US_x_A_12P:0.00732672):0.00596663,x_US_x_A_07C:0.00449846):0
101 .00639319,((((x_US_x_A_02P:-2.62303e-05,x_US_x_A_05P:0.00591507):0.
102 000156788,x_US_x_A_04P:0.00576826):0.00907366,((x_US_x_A_03P:0.00941548,
103 x_US_x_A_14P:0.00866127):0.00229499,x_US_x_A_13P:0.0209192):0.00469629):
104 0.0146758,(x_US_x_A_10P:0.000156443,x_US_x_A_15P:0.00578946):0.00472532)
105 :0.0103079):0.00733948):0.00228489,x_US_x_A_06P:0.00557974):0.00472981,
106 x_US_x_A_04C:0.00478858):0.00105548,x_US_x_A_05C:0.0120259):0.0060905,
107 x_US_x_A_12C:0.002911):2.90824e-05,x_US_x_A_11C:-5.79432e-06):4.34574e-
108 06,x_US_x_A_13C:-4.34574e-06):4.34574e-06,((x_US_x_A_08C:0.0029538,
109 x_US_x_A_09C:-1.31511e-05):0.00296627,x_US_x_A_10C:-8.69148e-06):4.
110 34574e-06,x_US_x_A_15C:-4.34574e-06);
111
112 Which can be partitioned into two groups of leaves, those that end in "P", and those that
113 end in "C"
114
115 1. Reg-exp 1: `P^`
116 2. Reg-exp 2: `C^`
117
118
119 Output
120 ------
121
122 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
123
124 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/Slatkin for an example)
125
126 Further reading
127 ---------------
128
129 https://github.com/veg/hyphy-analyses/tree/master/SlatkinMaddison
130
131
71 ]]></help> 132 ]]></help>
72 <expand macro="citations"> 133 <expand macro="citations">
73 <citation type="bibtex"> 134 <citation type="bibtex">
74 @UNPUBLISHED{slatkin, 135 @PUBLISHED{slatkin,
75 author = "Slatkin M, Maddison WP", 136 author = "Slatkin M, Maddison WP",
76 title = "A cladistic measure of gene flow inferred from the phylogenies of alleles", 137 title = "A cladistic measure of gene flow inferred from the phylogenies of alleles",
77 year = "1989", 138 year = "1989",
78 note = "Genetics 123(3):603-613", 139 note = "Genetics 123(3):603-613",
79 url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"} 140 url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"}