comparison phylogenomics_analysis.xml @ 17:7a6c7f3f9637 draft

Uploaded

16:4bb89dcc9642

 - **Select sequences classified into gene family clusters** - A history item with the label 'Sequences classified into gene family clusters on...'.
 - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
 - **Protein clustering method** - One of GFam, OrthoFinder or OrthoMCL.

 * **Multiple sequence alignments options**

 - **Select process for multiple sequence alignments** - Process used for setting multiple sequence alignments.
 - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that 'Yes' was selected for the 'Create orthogroup fasta files?' option on the GeneFamilyClassifier tool when generating the selected input.  This tool will produce an error if 'No' was selected.
 - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
 - **Sequence type used in the phylogenetic inference** - Sequence type used in the phylogenetic inference.
 - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that 'Yes' was selected for the 'Create corresponding coding sequences?' option on the GeneFamilyClassifier tool when generating the selected input.  This tool will produce an error if 'No' was selected.

 * **Phylogenetic trees options**

 - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
 - **Select history item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees?** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
 - **History item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees** -History item containing a set of string fragments matching sequences identifiers of species in the classification (including scaffold taxa) to be used for determining the most basal taxa in the orthogroups for rooting trees. The set of string fragments must be listed in decreasing order from older to younger lineages.
 - **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.
 - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments.
 - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments

* **MSA quality control options**

 - **Remove sequences with gaps of** - Removes gappy sequences in alignments (i.e., 0.5 removes sequences with 50% gaps).
 - **Select process used for gap trimming** - Either nucleotide based trimming or alignments are trimed using using trimAl's ML heuristic trimming approach.

17:7a6c7f3f9637

 - **Select sequences classified into gene family clusters** - A history item with the label 'Sequences classified into gene family clusters on...'.
 - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
 - **Protein clustering method** - One of GFam, OrthoFinder or OrthoMCL.

* **Multiple sequence alignments options**

 - **Select process for multiple sequence alignments** - Process used for setting multiple sequence alignments.
 - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that 'Yes' was selected for the 'Create orthogroup fasta files?' option on the GeneFamilyClassifier tool when generating the selected input.  This tool will produce an error if 'No' was selected.
 - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
 - **Sequence type used in the phylogenetic inference** - Sequence type used in the phylogenetic inference.
 - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that 'Yes' was selected for the 'Create corresponding coding sequences?' option on the GeneFamilyClassifier tool when generating the selected input.  This tool will produce an error if 'No' was selected.

* **Phylogenetic trees options**

 - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
 - **Select history item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees?** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
 - **History item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees** -History item containing a set of string fragments matching sequences identifiers of species in the classification (including scaffold taxa) to be used for determining the most basal taxa in the orthogroups for rooting trees. The set of string fragments must be listed in decreasing order from older to younger lineages.
 - **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.
 - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments.
 - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments.

* **MSA quality control options**

 - **Remove sequences with gaps of** - Removes gappy sequences in alignments (i.e., 0.5 removes sequences with 50% gaps).
 - **Select process used for gap trimming** - Either nucleotide based trimming or alignments are trimed using using trimAl's ML heuristic trimming approach.