---
name: "ktImportPhymmBL"
section: "1"
platform: "linux"
package: "radiant"
version: "2.8.1+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/ktImportPhymmBL"
---

# ktImportPhymmBL(1)

explore hierarchical metagenomic data with zoomable pie charts

## NAME

ktImportPhymmBL - explore hierarchical metagenomic data with zoomable pie charts

## DESCRIPTION

-

  Creates a Krona chart of Phymm or PhymmBL results. Note: Since confidence scores are not given for species/subspecies classifications, they inheret confidence scores from genus classifications.

-

  ktImportPhymmBL \\

-

  \[options\] \\ phymmbl\_results\_1\[:magnitudes\_1\]\[,name\_1\] \\ \[phymmbl\_results\_2\[:magnitudes\_2\]\[,name\_2\]\] \\ ...

- phymmbl\_results

  PhymmBL results files (results.03.\*). Results can also be from Phymm alone (results.01.\*), but \[-p\] must be specified. By default, separate datasets will be created for each input (see \[-c\]).

- magnitudes

  Optional file listing query IDs with magnitudes, separated by tabs. This can be used to account for read length or contig depth to obtain a more accurate representation of abundance. By default, query sequences without specified magnitudes will be assigned a magnitude of 1. Magnitude files for assemblies in ACE format can be created with ktGetContigMagnitudes.

- name

  A name to show in the list of datasets in the Krona chart (if multiple input files are present and \[-c\] is not specified). By default, the basename of the file will be used.

-

  - \[-o \<string\>\]

  Output file name. \[Default: 'phymm(bl).krona.html'\]

- \[-n \<string\>\]

  Name of the highest level. \[Default: 'all'\]

- \[-m \<number\>\]

  Minimum confidence. Each query sequence will only be added to taxa that were predicted with a confidence score of at least this value.

- \[-c\]

  Combine data from each file, rather than creating separate datasets within the chart.

- \[-d \<integer\>\]

  Maximum depth of wedges to include in the chart.

- \[-x \<integer\>\]

  Hue (0-360) for "bad" scores. \[Default: '0'\]

- \[-y \<integer\>\]

  Hue (0-360) for "good" scores. \[Default: '120'\]

- \[-p\]

  Input is phymm only (no confidence scores).

- \[-u \<string\>\]

  URL of Krona resources to use instead of bundling them with the chart (e.g. "http://krona.sourceforge.net"). Reduces size of charts and allows updates, though charts will not work without access to this URL.

- \[-qp \<string\>\]

  Url to send query IDs to (instead of listing them) for each wedge. The query IDs will be sent as a comma separated list in the POST variable "queries", with the current dataset index (from 0) in the POST variable "dataset". The url can include additional variables encoded via GET.