augur tree

Build a tree using a variety of methods.

usage: augur tree [-h] --alignment ALIGNMENT
                  [--method {fasttree,raxml,iqtree}] [--output OUTPUT]
                  [--substitution-model {HKY,GTR,HKY+G,GTR+G,GTR+R10}]
                  [--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


Possible choices: fasttree, raxml, iqtree

tree builder to use

Default: “iqtree”

--output, -o

file name to write tree to


Possible choices: HKY, GTR, HKY+G, GTR+G, GTR+R10

substitution model to use. Specify ‘none’ to run ModelTest. Currently, only available for IQTREE.

Default: “GTR”


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


fasta file of the sequence the VCF was mapped to


file name of one-based sites to exclude for raw tree building (BED format in .bed files, DRM format in tab-delimited files, or one position per line)


extra arguments to be passed directly to the executable of the requested tree method (e.g., –tree-builder-args=”-czb”)

Default: “”