|Description:|| Mapping taxonomic groups onto sequences based on Newick trees.|
|Last Edit:|| 08/01/19|
Copyright © 2016 Richard J. Edwards - See source code for GNU License Notice
See SLiMSuite Blog for further documentation. See
rje for general commands.
nwklist=FILES : List of Newick format files. (*.nwk names must match accnum.) Wildcards allowed. [
protdesc=FILE : Delimited file of protein, description [
classify=FILELIST : List of files containing protein IDs (first column) for additional taxsum outputs [
basefile=X : Base for output files. Will reuse unless
taxbase=X : Base of previous run to load results from, if not basefile 
Taxon Assignment Options
minboot=X : Minimum bootstrap value for an "in-clade" with query protein [
noneboot=X : Bootstrap support to give "None" ratings [
minscore=X : Filter out species codes with score < minscore [
minsum=X : Convert taxa with score < minsum to "Other" for *.taxsum.tdt output [
minclass=X : Convert taxa with score < minclass to "Other" for *.CLASS.tdt output [
bootweight=T/F : Whether to weight taxon scores for each protein by clade bootstrap support for filtering [
bootfilter=X : Filter bootstrap support < X to "Uncertain" [
monophyly=T/F : Enforce strict monophyly and change any multiple assignments to "Uncertain" [
taxfilter=LIST : List of taxonomic assignments to filter from rank/summary (e.g. "Uncertain") 
History Module Version History
# 0.0.0 - Initial Compilation.
# 0.1.0 - Initial Working Version.
# 0.2.0 - Added bootstraps and minscore.
# 0.2.1 - Fixed missing species names in *.taxa.tdt output.
# 0.3.0 - Added monophyly=T/F : Enforce strict monophyly and change any multiple assignments to "Uncertain" [False]
# 0.4.0 - Added TaxFilter, minsum=X and classify=FILELIST files containing protein IDs (first column) for additional taxsum outputs [*.class]
# 0.5.0 - Fixed the filtering of Unmapped taxa when other (mapped) taxa are present.
# 0.5.1 - Minor bug fix for classes with blank lines.