Mercurial > repos > greg > kaks_analysis
comparison kaks_analysis.xml @ 31:9b78e5c2a14e draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 01 May 2017 12:51:04 -0400 |
| parents | c91e1673c8e7 |
| children | 9821735dccc4 |
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| 30:715ca3160a27 | 31:9b78e5c2a14e |
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| 217 - **Protein sequences for the second species** - corresponding protein sequence fasta files for the second species either produced by the AssemblyPostProcessor tool or from an external source selected from your history. This option is required only for orthologous comparison. | 217 - **Protein sequences for the second species** - corresponding protein sequence fasta files for the second species either produced by the AssemblyPostProcessor tool or from an external source selected from your history. This option is required only for orthologous comparison. |
| 218 - **Alignment coverage configuration** - select 'Yes' to set the minimum allowable alignment coverage length between homologous pairs. PlantTribes uses global codon alignment match score to determine the pairwise alignment coverage. By default, the match score is set to 0.5 if 'No' is selected. | 218 - **Alignment coverage configuration** - select 'Yes' to set the minimum allowable alignment coverage length between homologous pairs. PlantTribes uses global codon alignment match score to determine the pairwise alignment coverage. By default, the match score is set to 0.5 if 'No' is selected. |
| 219 | 219 |
| 220 - **match score** - number of base matches in a pairwise sequence alignment divided by the length of shorter sequence. Positions in the alignment corresponding to gaps are not considered. The score is restricted to the range 0.3 - 1.0. | 220 - **match score** - number of base matches in a pairwise sequence alignment divided by the length of shorter sequence. Positions in the alignment corresponding to gaps are not considered. The score is restricted to the range 0.3 - 1.0. |
| 221 | 221 |
| 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. Rate recalibration 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 [7]. Rate recalibration 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). | 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). |
| 289 year = {1999}, | 289 year = {1999}, |
| 290 volume = {4}, | 290 volume = {4}, |
| 291 number = {2}, | 291 number = {2}, |
| 292 pages = {1-14},} | 292 pages = {1-14},} |
| 293 </citation> | 293 </citation> |
| 294 <citation type="bibtex"> | |
| 295 @article{Cui2006, | |
| 296 journal = {Genome Research}, | |
| 297 author = {7. Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, Albert VA}, | |
| 298 title = {Widespread genome duplications throughout the history of flowering plants}, | |
| 299 year = {2006}, | |
| 300 volume = {16}, | |
| 301 number = {6}, | |
| 302 pages = {738-749},} | |
| 303 </citation> | |
| 294 </citations> | 304 </citations> |
| 295 </tool> | 305 </tool> |