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Change default iqmodel to GTR

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trvrb committed Jul 5, 2018
1 parent 8680b3e commit b018d8d77431feef7c484c1619033d48b5478084
Showing with 2 additions and 2 deletions.
  1. +1 −1 augur/
  2. +1 −1 bin/augur
@@ -94,7 +94,7 @@ def build_fasttree(aln_file, out_file, clean_up=True):
return T
def build_iqtree(aln_file, out_file, substitution_model="GTR+G", clean_up=True, nthreads=2):
def build_iqtree(aln_file, out_file, substitution_model="GTR", clean_up=True, nthreads=2):
build tree using IQ-Tree with parameters "-fast"
@@ -61,7 +61,7 @@ if __name__=="__main__":
tree_parser.add_argument('--alignment', '-a', required=True, help="alignment in fasta or VCF format")
tree_parser.add_argument('--method', default='iqtree', choices=["fasttree", "raxml", "iqtree"], help="tree builder to use")
tree_parser.add_argument('--output', '-o', type=str, help='file name to write tree to')
tree_parser.add_argument('--substitution-model', default="GTR+G", choices=["HKY", "GTR", "HKY+G", "GTR+G"],
tree_parser.add_argument('--substitution-model', default="GTR", choices=["HKY", "GTR", "HKY+G", "GTR+G"],
help='substitution model to use. Specify \'none\' to run ModelTest. Currently, only available for IQTREE.')
tree_parser.add_argument('--nthreads', type=int, default=2,
help="number of threads used")

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