Mercurial > repos > greg > kaks_analysis
comparison kaks_analysis.xml @ 28:b807167c1e60 draft
Uploaded
| author | greg |
|---|---|
| date | Fri, 28 Apr 2017 14:30:26 -0400 |
| parents | f174450ebc44 |
| children | c91e1673c8e7 |
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| 27:f174450ebc44 | 28:b807167c1e60 |
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| 222 - **Species rates recalibration configuration** - select 'Yes' to recalibrate synonymous substitution rates of a species using a predetermined evolutionary rate. Recalibration evolutionary rate can be determined from a species tree inferred from a collection of conserved single copy genes from taxa of interest as described in Cui et al., 2006. Applies only to paralogous comparisons. | 222 - **Species rates recalibration configuration** - select 'Yes' to recalibrate synonymous substitution rates of a species using a predetermined evolutionary rate. Recalibration evolutionary rate can be determined from a species tree inferred from a collection of conserved single copy genes from taxa of interest as described in Cui et al., 2006. Applies only to paralogous comparisons. |
| 223 | 223 |
| 224 - **recalibration rate** - a predetermined evolutionary recalibration rate. | 224 - **recalibration rate** - a predetermined evolutionary recalibration rate. |
| 225 | 225 |
| 226 - **PAML codeml configuration** - select 'Yes' to enable selection of a PAML codeml control file to carry out maximum likelihood analysis of protein-coding DNA sequences using codon substitution models. Template file "codeml.ctl.args" can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and are also available at the PlantTribes GitHub `repository`_. Default settings shown in the template are used if 'No' is selected. | 226 - **PAML codeml configuration** - select 'Yes' to enable selection of a PAML codeml control file to carry out maximum likelihood analysis of protein-coding DNA sequences using codon substitution models. Template file "codeml.ctl.args" can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and are also available at the PlantTribes GitHub `repository`_. Default settings shown in the template are used if 'No' is selected. |
| 227 - **Rates clustering configuration** - select 'Yes' to estimate clusters of synonymous substitution rates using a mixture of multivariate normal distributions which represent putative duplication event(s). | |
| 228 | |
| 229 - **Number of components** - number of components to include in the normal mixture model. | |
| 230 | |
| 231 - **Lower limit synonymous subsitution rates configuration** - select 'Yes' to set the minimum allowable synonymous substitution rate to use in the normal mixtures cluster analysis to exclude young paralogs that arise from normal gene births and deaths in a genome. | |
| 232 | |
| 233 - **Minimum rate** - minimum allowable synonymous substitution rate. | |
| 234 | |
| 235 - **Upper limit synonymous subsitution rates configuration** - select 'Yes' to set the maximum allowable synonymous substitution rate to use in the normal mixtures cluster analysis to exclude likely ancient paralogs in a genome. | |
| 236 | |
| 237 - **Maximum rate** - maximum allowable synonymous substitution rate. | |
| 227 | 238 |
| 228 .. _repository: https://github.com/dePamphilis/PlantTribes/blob/master/config/codeml.ctl.args | 239 .. _repository: https://github.com/dePamphilis/PlantTribes/blob/master/config/codeml.ctl.args |
| 229 | |
| 230 - **Rates clustering configuration** - select 'Yes' to estimate clusters of synonymous substitution rates using a mixture of multivariate normal distributions which represent putative duplication event(s). | |
| 231 | |
| 232 - **Number of components** - number of components to include in the normal mixture model. | |
| 233 | |
| 234 - **Lower limit synonymous subsitution rates configuration** - select 'Yes' to set the minimum allowable synonymous substitution rate to use in the normal mixtures cluster analysis to exclude young paralogs that arise from normal gene births and deaths in a genome. | |
| 235 | |
| 236 - **Minimum rate** - minimum allowable synonymous substitution rate. | |
| 237 | |
| 238 - **Upper limit synonymous subsitution rates configuration** - select 'Yes' to set the maximum allowable synonymous substitution rate to use in the normal mixtures cluster analysis to exclude likely ancient paralogs in a genome. | |
| 239 | |
| 240 | |
| 241 - **Maximum rate** - maximum allowable synonymous substitution rate. | |
| 242 | 240 |
| 243 </help> | 241 </help> |
| 244 <citations> | 242 <citations> |
| 245 <expand macro="citation1" /> | 243 <expand macro="citation1" /> |
| 246 <citation type="bibtex"> | 244 <citation type="bibtex"> |