augur.tree module

Build a tree using a variety of methods.

augur.tree.build_fasttree(aln_file, out_file, clean_up=True, nthreads=1, tree_builder_args='')

build tree using fasttree with parameters “-nt”

augur.tree.build_iqtree(aln_file, out_file, substitution_model='GTR', clean_up=True, nthreads=1, tree_builder_args='')

build tree using IQ-Tree with parameters “-fast” :param aln_file file name of input aligment: :param out_file file name to write tree to:

augur.tree.build_raxml(aln_file, out_file, clean_up=True, nthreads=1, tree_builder_args='')

build tree using RAxML with parameters ‘-f d -m GTRCAT -c 25 -p 235813 -n tre”

augur.tree.find_executable(names, default=None)

Return the path to the first executable found in PATH from the given list of names.

Raises a (hopefully helpful) error if no executable is found. Provide a value for the “default” parameter to instead return a value.

augur.tree.mask_sites_in_multiple_sequence_alignment(alignment_file, excluded_sites_file)

Creates a new multiple sequence alignment FASTA file from which the given excluded sites have been removed and returns the filename of the new alignment.

Parameters
  • alignment_file (str) – path to the original multiple sequence alignment file

  • excluded_sites_file (str) – path to a text file containing each nucleotide position to exclude with one position per line

Returns

path to the new FASTA file from which sites have been excluded

Return type

str

augur.tree.register_arguments(parser)
augur.tree.run(args)
augur.tree.write_out_informative_fasta(compress_seq, alignment, stripFile=None)