necom Documentation

Scan Dynamic Tree Cut min cluster sizes.

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:

• The --range option is required and must be start,end,step with comma separators and no spaces.
• All three range values must be non-negative integers and the step must be positive.
• start must be at least 1 because the min cluster size must be greater than 0.
• --deep-split enables more aggressive splitting (default: off).
• --max-tree-height sets the maximum joining height; if omitted, 99% of the tree height is used.
• --support <S> treats edges with support < S as effectively infinite length.
• The --format and --rep options are not available in scan mode.
• The output Group column is labeled dynamic-tree=<min-size>.

Examples:

1. Scan min cluster sizes from 2 to 20 necom cut scan-dynamic tree.nwk --range 2,20,2 --stats-out stats.tsv > partitions.tsv

2. Scan with deep split enabled necom cut scan-dynamic tree.nwk --range 2,20,2 --deep-split --stats-out stats.tsv > partitions.tsv