augur tree

Build a tree using a variety of methods.

IQ-TREE specific: Strain names with spaces are modified to remove all characters after (and including) the first space.

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]
                  [--override-default-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 IQ-TREE.

Default: 'GTR'

--nthreads

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

--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

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=”–polytomy” 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 –epsilon 0.05 -T AUTO –redo”.

Note that IQ-TREE will rewrite certain characters in FASTA deflines. In order to prevent this from breaking downstream analysis steps, augur tree preemptively rewrites conflicting deflines, and then restores them later. Unfortunately, this breaks the use of certain IQ-TREE options (e.g., -g) which rely on matching names between the FASTA and other input files.

--override-default-args

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>”