Returns list of species in a phylogenetic tree ordered by increasing taxonomic distance to a reference species
Project description
usage: taxOrder.py [-h] -t -r str [--outfile [str]] [--format [str]] [--idmap []]
Returns list of species in a phylogenetic tree ordered by increasing taxonomic distance to a reference species
-h, --help show this help message and exit
-t , --tree Path to tree in Newick format
-r , --reference str Reference species
optional arguments:
--outfile [str] Save output to file
--format [str] Tree format as specified at: https://etetoolkit.org/docs/latest/tutorial/tutorial_trees.html#reading-and-writing-newick-trees (Default: 1)
--idmap [] TaxOrder can map species names to taxids accepted by PhyloProfile if supplied with a tab-seperated file like: taxid name
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