augur tree¶
Build a tree using a variety of methods.
usage: augur tree [-h] --alignment ALIGNMENT
[--method {fasttree,raxml,iqtree}] [--output OUTPUT]
[--substitution-model SUBSTITUTION_MODEL]
[--nthreads NTHREADS] [--vcf-reference VCF_REFERENCE]
[--exclude-sites EXCLUDE_SITES]
[--tree-builder-args TREE_BUILDER_ARGS]
Named Arguments¶
- --alignment, -a
alignment in fasta or VCF format
- --method
Possible choices: fasttree, raxml, iqtree
tree builder to use
Default: “iqtree”
- --output, -o
file name to write tree to
- --substitution-model
substitution model to use. Specify ‘auto’ to run ModelTest. Currently, only available for IQTREE.
Default: “GTR”
- --nthreads
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
Default: 1
- --vcf-reference
fasta file of the sequence the VCF was mapped to
- --exclude-sites
file name of one-based sites to exclude for raw tree building (BED format in .bed files, second column in tab-delimited files, or one position per line)
- --tree-builder-args
extra arguments to be passed directly to the executable of the requested tree method (e.g., –tree-builder-args=”-czb”)
Default: “”