necom Documentation

Scan static threshold cut parameters.

Input:

• A Newick file containing a single tree.

Output:

• Always writes the long format table Group\tClusterID\tSampleID.
• If --stats-out is given, also writes a summary table with Group\tClusters\tSingletons\tNon-Singletons\tMaxSize.

Notes:

• Exactly one method flag must be provided: --k, --height, --root-dist, --max-clade, --avg-clade, --med-clade, --sum-branch, --leaf-dist-max, --leaf-dist-min, --leaf-dist-avg, --max-edge (--single-linkage), --inconsistent.
• --range is required and must be start,end,step with comma separators and no spaces.
• --k --range requires integer values and the start must be at least 1.
• --deep controls the depth for the inconsistent method (default: 2).
• Distance/height thresholds must be non-negative finite numbers.
• --support <S> treats edges with support < S as effectively infinite length.
• The --format and --rep options are not available in scan mode.

Examples:

1. Scan heights and save statistics necom cut scan-simple tree.nwk --height --range 0,1.0,0.05 --stats-out stats.tsv > partitions.tsv

2. Scan max-clade thresholds necom cut scan-simple tree.nwk --max-clade --range 0,0.5,0.01

3. Scan cluster counts necom cut scan-simple tree.nwk --k --range 1,5,1