augur treeļ
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 Argumentsļ
- --alignment, -a
alignment in fasta or VCF format
- --method
Possible choices: fasttree, raxml, iqtree
tree builder to use
Default: āiqtreeā
- --output, -o
file name to write tree to
- --substitution-model
substitution model to use. Specify āautoā to run ModelTest. Currently, only available for IQTREE.
Default: āGTRā
- --nthreads
number of threads to use; specifying the value āautoā 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., ātree-builder-args=ā-czbā for IQ-TREE) to avoid unexpected errors. FastTree defaults: ā-nt -nosupportā. RAxML defaults: ā-f d -m GTRCAT -c 25 -p 235813ā. IQ-TREE defaults: ā-ninit 2 -n 2 -me 0.05ā.
- --override-default-args
override default tree builder arguments with the values provided by the user in ātree-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 āmethod iqtree āalignment <alignment> āsubstitution-model <model> āoutput <tree> ātree-builder-args=ā<extra arguments>ā