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augur/ allow additional models, relax version requi…

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rneher committed Jun 7, 2019
1 parent 9aff33c commit 8401acbd94034a099576372138471e078a930d11
Showing with 3 additions and 3 deletions.
  1. +1 −1 augur/
  2. +2 −2
@@ -357,7 +357,7 @@ def register_arguments(parser):
parser.add_argument('--alignment', '-a', required=True, help="alignment in fasta or VCF format")
parser.add_argument('--method', default='iqtree', choices=["fasttree", "raxml", "iqtree"], help="tree builder to use")
parser.add_argument('--output', '-o', type=str, help='file name to write tree to')
parser.add_argument('--substitution-model', default="GTR", choices=["HKY", "GTR", "HKY+G", "GTR+G"],
parser.add_argument('--substitution-model', default="GTR", choices=["HKY", "GTR", "HKY+G", "GTR+G", "GTR+R10"],
help='substitution model to use. Specify \'none\' to run ModelTest. Currently, only available for IQTREE.')
parser.add_argument('--nthreads', type=nthreads_value, default=1,
help="number of threads to use; specifying the value 'auto' will cause the number of available CPU cores on your system, if determinable, to be used")
@@ -40,9 +40,9 @@
"ipdb >=0.10.1",
"jsonschema ==3.0.0a3",
"matplotlib >=2.0, ==2.*",
"pandas >=0.23.4, ==0.23.*",
"pandas >=0.23.4",
"phylo-treetime >=0.5.6, ==0.5.*",
"seaborn >=0.9.0, ==0.9.*",
"seaborn >=0.9.0",
"snakemake >=5.1.5, ==5.*"

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