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]
                  [--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”.

--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>”