# HG changeset patch # User greg # Date 1493404857 14400 # Node ID b7b1d6ebcfd45c3fa296d10a9b819fa1bb0998d0 # Parent 7f8c1e115de859458373e96be6c9135e6af41830 Uploaded diff -r 7f8c1e115de8 -r b7b1d6ebcfd4 gene_family_phylogeny_builder.xml --- 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 +