Mercurial > repos > greg > gene_family_phylogeny_builder
changeset 9:b7b1d6ebcfd4 draft
Uploaded
| author | greg |
|---|---|
| date | Fri, 28 Apr 2017 14:40:57 -0400 |
| parents | 7f8c1e115de8 |
| children | 576278ba0dc4 |
| files | gene_family_phylogeny_builder.xml |
| diffstat | 1 files changed, 2 insertions(+), 3 deletions(-) [+] |
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--- a/gene_family_phylogeny_builder.xml Fri Apr 28 13:59:32 2017 -0400 +++ b/gene_family_phylogeny_builder.xml Fri Apr 28 14:40:57 2017 -0400 @@ -158,13 +158,12 @@ **Other options** * **Rooting order configuration** - select 'Yes' to enable selection of a rooting order configuration file for RAxML. Scaffold configuration templates (.rootingOrder.config) of how to customize the RAxML ML tree rooting order can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and is also available at the PlantTribes GitHub `repository`_. Phylogenetic tree rooting order settings shown in these templates are used as defaults if 'No' is selected. - -.. _repository: https://github.com/dePamphilis/PlantTribes/tree/master/config - * **Bootstrap replicates** - number of bootstrap replicates for RAxML to conduct a rapid bootstrap analysis and search for the best-scoring ML tree (default = 100). * **Maximum orthogroup size** - Maximum number of sequences allowed in orthogroup alignments (default = 100). * **Minimum orthogroup size** - Minimum number of sequences allowed in orthogroup alignments (default = 4). +.. _repository: https://github.com/dePamphilis/PlantTribes/tree/master/config + </help> <citations> <expand macro="citation1" />