A Groovy map containing sample information,
e.g. [ id: “test” ]
infile:file
MSA or distance matrix in Phylip format
*
initial_tree:file
Initial tree
Output
name:type
description
pattern
nwk
meta:file
Final phylogeny in Newick format
*.nwk
*.nwk:file
Final phylogeny in Newick format
*.nwk
stats
meta:file
A text file with the statistics of the phylogeny
*_stat.txt
*_stat.txt:file
A text file with the statistics of the phylogeny
*_stat.txt
matrix
meta: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
*.matrix.phy: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
meta: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
*.bootstrap
*.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
*.bootstrap
versions
versions.yml:file
File containing software versions
versions.yml
Tools
fastme
GPL v3
A comprehensive, accurate and fast distance-based phylogeny inference program.
