Construct a phylogenetic tree with bootstrap supports using RAxML.
Construct a phylogenetic tree with RAxML with the addition of rapid
bootstrapping support values. See:
https://sco.h-its.org/exelixis/web/software/raxml/
Parameters
- alignment : FeatureData[AlignedSequence]
- Aligned sequences to be used for phylogenetic reconstruction.
- seed : Int, optional
- Random number seed for the parsimony starting tree. This allows you to
reproduce tree results. If not supplied then one will be randomly
chosen.
- rapid_bootstrap_seed : Int, optional
- Specify a random seed for rapid bootstrapping. This allows you to
reproduce rapid bootstrap results. If not supplied then one will be
randomly chosen.
- bootstrap_replicates : Int % Range(10, None), optional
- The number of bootstrap searches to perform.
- raxml_version : Str % Choices('Standard', 'SSE3', 'AVX2'), optional
- Select a specific CPU optimization of RAxML to use. The SSE3 versions
will run approximately 40% faster than the standard version. The AVX2
version will run 10-30% faster than the SSE3 version.
- substitution_model : Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI'), optional
- Model of Nucleotide Substitution
Returns
- tree : Phylogeny[Unrooted]
- The resulting phylogenetic tree.