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comparison phylogenomics_analysis.xml @ 70:bd26a18387ae draft

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author greg
date Thu, 16 Mar 2017 14:31:52 -0400
parents 34dcfb570551
children 43e5db9461cf
comparison
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69:34dcfb570551 70:bd26a18387ae
1 <tool id="plant_tribes_phylogenomics_analysis" name="Create multiple sequence alignments" version="0.6.0"> 1 <tool id="plant_tribes_phylogenomics_analysis" name="PhylogenomicsAnalysis" version="0.6.0">
2 <description>and inferred maximum likelihood phylogenies</description> 2 <description>builds gene family multiple sequence alignments and their corresponding phylogenies</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.6">plant_tribes_phylogenomics_analysis</requirement> 4 <requirement type="package" version="0.6">plant_tribes_phylogenomics_analysis</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <!-- Anything other than zero is an error --> 7 <!-- Anything other than zero is an error -->
295 - **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). 295 - **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).
296 296
297 </help> 297 </help>
298 <citations> 298 <citations>
299 <citation type="bibtex"> 299 <citation type="bibtex">
300 @unpublished{None, 300 @misc{None,
301 author = {Eric Wafula}, 301 journal = {None},
302 title = {None}, 302 author = {1. Wafula EK},
303 title = {Manuscript in preparation},
303 year = {None}, 304 year = {None},
304 url = {https://github.com/dePamphilis/PlantTribes} 305 url = {https://github.com/dePamphilis/PlantTribes},}
305 }
306 </citation>
307 <citation type="doi">10.1093/bioinformatics/btw412</citation>
308 <citation type="bibtex">
309 @published{Research in Computational Molecular Biology (RECOMB) (pp. 177–191),
310 author = {Mirarab, S., Nguyen, N., Warnow, T.},
311 title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan
312 (Ed.)},
313 year = {2014},
314 url = {https://github.com/smirarab/pasta}
315 }
316 </citation> 306 </citation>
317 <citation type="bibtex"> 307 <citation type="bibtex">
318 @published{Bioinformatics, 308 @article{Mirarab2014,
319 author = {Salvador Capella-Gutierrez, Jose M. Silla-Martinez, Toni 309 journal = {Research in Computational Molecular Biology (RECOMB)},
320 Gabaldon}, 310 author = {2. Mirarab S, Nguyen N, Warnow T},
321 title = {trimAl: a tool for automated alignment trimming in large-scale 311 title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan (Ed.)},
322 phylogenetic analyses}, 312 year = {2014},
323 year = {2009}, 313 pages = {177–191},
324 url = {http://trimal.cgenomics.org} 314 url = {https://github.com/smirarab/pasta},}
325 }
326 </citation> 315 </citation>
327 <citation type="bibtex"> 316 <citation type="bibtex">
328 @published{Bioinformatics, 317 @article{Salvador2009,
329 author = {A. Stamatakis}, 318 journal = {Bioinformatics},
330 title = {RAxML Version 8: A tool for Phylogenetic Analysis and 319 author = {3. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T},
331 Post-Analysis of Large Phylogenies}, 320 title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
321 year = {2009},
322 url = {http://trimal.cgenomics.org},}
323 </citation>
324 <citation type="bibtex">
325 @article{Stamatakis2014,
326 journal = {Bioinformatics},
327 author = {4. Stamatakis A},
328 title = {RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies},
332 year = {2014}, 329 year = {2014},
333 url = {http://sco.h-its.org/exelixis/web/software/raxml/index.html} 330 url = {http://sco.h-its.org/exelixis/web/software/raxml/index.html},}
334 }
335 </citation> 331 </citation>
336 <citation type="doi">10.1371/journal.pone.0009490</citation> 332 <citation type="doi">10.1371/journal.pone.0009490</citation>
333 <citation type="doi">10.1093/bioinformatics/btw412</citation>
337 </citations> 334 </citations>
338 </tool> 335 </tool>