Mercurial > repos > dcorreia > phyml_sms_1_3

comparison phyml_sms.xml @ 18:b347bcd7304e draft default tip

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author dcorreia
date Mon, 26 Sep 2016 11:15:20 -0400
parents 79998c33aa5a
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17:79998c33aa5a 18:b347bcd7304e
114 114
115 .. class:: infomark 115 .. class:: infomark
116 116
117 This script runs SMS to select the substitution model which best fits the input data. 117 This script runs SMS to select the substitution model which best fits the input data.
118 It may also run PhyML with the selected model. 118 It may also run PhyML with the selected model.
119 SMS options : 119
120 SMS options ::
121
120 -h = Help 122 -h = Help
121 -i = **Mandatory** Input alignment file in PHYLIP format 123 -i = **Mandatory** Input alignment file in PHYLIP format
122 -d = **Mandatory** Data type : 'aa' or 'nt' 124 -d = **Mandatory** Data type : 'aa' or 'nt'
123 -o = Output directory 125 -o = Output directory
124 -p = Output CSV filename 126 -p = Output CSV filename
125 -c = Statistical criterion to select the model : 'AIC' (default) or 'BIC' 127 -c = Statistical criterion to select the model : 'AIC' (default) or 'BIC'
126 -u = Input starting tree (Newick format) 128 -u = Input starting tree (Newick format)
127 -t = Use this option if you want SMS to infer a tree with PhyML using the SMS selected model 129 -t = Use this option if you want SMS to infer a tree with PhyML using the SMS selected model
128 PhyML options : 130
131 PhyML options ::
132
129 -s = Type of tree improvement : 'NNI (default)' or 'SPR' 133 -s = Type of tree improvement : 'NNI (default)' or 'SPR'
130 -r = Number of random starting trees : 0 (default) 134 -r = Number of random starting trees : 0 (default)
131 -b = Branch Support : >0 for bootstraps, -4 for aLRT, 0 (default) 135 -b = Branch Support : >0 for bootstraps, -4 for aLRT, 0 (default)
136
132 137
133 **PhyML 20120412** 138 **PhyML 20120412**
134 139
135 ----- 140 -----
136 141