augur.tree module¶
Build a tree using a variety of methods.
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augur.tree.
build_fasttree
(aln_file, out_file, clean_up=True, nthreads=1, tree_builder_args='')¶ build tree using fasttree with parameters “-nt”
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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:
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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”
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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.
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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
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augur.tree.
register_arguments
(parser)¶
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augur.tree.
run
(args)¶
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augur.tree.
write_out_informative_fasta
(compress_seq, alignment, stripFile=None)¶