Examples

This section contains various code snippets that demonstrate scphylo’s usage.

Reconstruction

Below is a gallery of examples for reconstructing tumor phylogeny using available tools in scphylo.tl.

PhISCS-BnB reconstruction.

PhISCS-BnB reconstruction.

Trisicell-Boost reconstruction.

Trisicell-Boost reconstruction.

GPPS reconstruction.

GPPS reconstruction.

HUNTRESS reconstruction.

HUNTRESS reconstruction.

OncoNEM reconstruction.

OncoNEM reconstruction.

PhISCS reconstruction.

PhISCS reconstruction.

ScisTree reconstruction.

ScisTree reconstruction.

SCITE reconstruction.

SCITE reconstruction.

SiCloneFit reconstruction.

SiCloneFit reconstruction.

SPhyR reconstruction.

SPhyR reconstruction.

Comparison

Below is a gallery of examples for comparing two phylogenetic trees using available tools in scphylo.tl.

Ancestor-descendent comparison.

Ancestor-descendent comparison.

CASet comparison.

CASet comparison.

DISC comparison.

DISC comparison.

Different-lineage comparison.

Different-lineage comparison.

Genotype-similarity comparison.

Genotype-similarity comparison.

MLTD comparison.

MLTD comparison.

MP3 comparison.

MP3 comparison.

Robinson-Foulds comparison.

Robinson-Foulds comparison.

TPTED comparison.

TPTED comparison.

Assessment

Below is a gallery of examples for assessing the inferred phylogenetic tree using functions in scphylo.tl.

Trisicell-PartF assessment.

Trisicell-PartF assessment.

Visualization

Below is a gallery of examples for visualizing the inferred phylogenetic tree using functions in scphylo.pl.

Clonal tree visualization.

Clonal tree visualization.

Dendrogram tree visualization.

Dendrogram tree visualization.