A Groovy map containing sample information,
e.g. [ id: “test” ]
infile (file)
MSA or distance matrix in Phylip format
*
topo (file)
Initial tree topology in Newick format
*.{nwk,dnd}
Output
Name (Type)
Description
Pattern
versions (file)
File containing software versions
versions.yml
nwk (file)
Final phylogeny in Newick format
*.nwk
stats (file)
A text file with the statistics of the phylogeny
*_stat.txt
matrix (file)
Optional; the distance matrix in Phylip matrix format; it is generated if the -O option is passed in ext.args, although the provided file name will be overwritten
*.matrix.phy
bootstrap (file)
A file containing all bootstrap trees in Newick format; it is generated if the -B option is passed in ext.args (and bootstrap is used), although the provided file name will be overwritten
