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comparison phylogenomics_analysis.xml @ 59:963f84101cdc draft

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author greg
date Wed, 15 Feb 2017 07:59:49 -0500
parents 1b256588fb06
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58:1b256588fb06 59:963f84101cdc
298 <tests> 298 <tests>
299 <test> 299 <test>
300 </test> 300 </test>
301 </tests> 301 </tests>
302 <help> 302 <help>
303 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of 303 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
304 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic 304 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
305 analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produced by the 305 analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produced by the
306 **Classify gene sequences into precomputed orthologous gene family clusters** tool. 306 **Classify gene sequences into precomputed orthologous gene family clusters** tool.
307 307
308 ----- 308 -----
309 309
310 **Options** 310 **Options**
311 311
312 * **Required options** 312 * **Required options**
313 313
314 - **Select gene family clusters** - Sequences classified into gene family clusters, optionally including corresponding coding sequences. 314 - **Select gene family clusters** - Sequences classified into gene family clusters, optionally including corresponding coding sequences.
315 - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data. 315 - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
316 - **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters). 316 - **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
317 * **Multiple sequence alignments options** 317
318 318 * **Multiple sequence alignments options**
319 - **Select method for multiple sequence alignments** - Method used for setting multiple sequence alignments. 319
320 - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs'. 320 - **Select method for multiple sequence alignments** - Method used for setting multiple sequence alignments.
321 - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments. 321 - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs'.
322 - **Sequence type used in the phylogenetic inference** - Sequence type (dna or amino acid) used in the phylogenetic inference. 322 - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
323 - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs' or this tool will produce an error. 323 - **Sequence type used in the phylogenetic inference** - Sequence type (dna or amino acid) used in the phylogenetic inference.
324 324 - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs' or this tool will produce an error.
325 * **Phylogenetic trees options** 325
326 326 * **Phylogenetic trees options**
327 - **Phylogenetic trees inference method** - Phylogenetic trees inference method. 327
328 - **Select rooting order configuration for rooting trees??** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup. 328 - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
329 - **Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree** - Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree. 329 - **Select rooting order configuration for rooting trees??** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
330 - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments. 330 - **Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree** - Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree.
331 - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments. 331 - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments.
332 332 - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments.
333 * **MSA quality control options** 333
334 334 * **MSA quality control options**
335 - **Remove sequences with gaps of** - Removes gappy sequences in alignments (i.e., 0.5 removes sequences with 50% gaps). 335
336 - **Select process used for gap trimming** - Either nucleotide based trimming or alignments are trimed using using trimAl's ML heuristic trimming approach. 336 - **Remove sequences with gaps of** - Removes gappy sequences in alignments (i.e., 0.5 removes sequences with 50% gaps).
337 - **Remove sites in alignments with gaps of** - If the process used for gap trimming is nucleotide based, this is the gap value used when removing gappy sites in alignments (i.e., 0.1 removes sites with 90% gaps). 337 - **Select process used for gap trimming** - Either nucleotide based trimming or alignments are trimed using using trimAl's ML heuristic trimming approach.
338 - **Remove sites in alignments with gaps of** - If the process used for gap trimming is nucleotide based, this is the gap value used when removing gappy sites in alignments (i.e., 0.1 removes sites with 90% gaps).
338 339
339 </help> 340 </help>
340 <citations> 341 <citations>
341 <citation type="bibtex"> 342 <citation type="bibtex">
342 @unpublished{None, 343 @unpublished{None,