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


Possible choices: fasttree, raxml, iqtree

tree builder to use

Default: “iqtree”

--output, -o

file name to write tree to


substitution model to use. Specify ‘auto’ to run ModelTest. Currently, only available for IQ-TREE.

Default: “GTR”


maximum 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, second column in tab-delimited files, or one position per line)

arguments to pass to the tree builder either augmenting or overriding the default arguments (except for input alignment path, number of threads, and substitution model).

Use the assignment operator (e.g., –tree-builder-args=”-czb” for IQ-TREE) to avoid unexpected errors. FastTree defaults: “-nt -nosupport”. RAxML defaults: “-f d -m GTRCAT -c 25 -p 235813”. IQ-TREE defaults: “-ninit 2 -n 2 -me 0.05 -nt AUTO -redo”.


override default tree builder arguments with the values provided by the user in –tree-builder-args instead of augmenting the existing defaults.

Default: False

For example, to build a tree with IQ-TREE, use the following format:

augur tree –method iqtree –alignment <alignment> –substitution-model <model> –output <tree> –tree-builder-args=”<extra arguments>”