IQTree Documentation¶
IQTree is a fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood.
Read more about iqtree at their github repository.
Examples¶
Using the commandline wrapper¶
By default, iqtree wil auto-detect a datatype. You can also specify a
datatype. You can select a datatype from the following list: BIN,
DNA, AA, NT2AA, CODON, MORPH.
from OrthoEvol.Orthologs.Phylogenetics import IQTreeCommandline
IQTreeCommandline(alignment='path/to/alignment/file')
Using the FilteredTree class¶
The FilteredTree class simply returns the best tree (which is determined by IQTree’s algorithm).
from OrthoEvol.Orthologs.Phylogenetics import FilteredTree
FilteredTree(alignment, dataType='CODON', working_dir='path/of/working/directory')
