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.

Reconstruct tree by PhISCS-BnB

Reconstruct tree by PhISCS-BnB

Reconstruct tree by Trisicell-Boost

Reconstruct tree by Trisicell-Boost

Reconstruct tree by gpps

Reconstruct tree by gpps

Reconstruct tree by OncoNEM

Reconstruct tree by OncoNEM

Reconstruct tree by PhISCS

Reconstruct tree by PhISCS

Reconstruct tree by ScisTree

Reconstruct tree by ScisTree

Reconstruct tree by SCITE

Reconstruct tree by SCITE

Reconstruct tree by SiCloneFit

Reconstruct tree by SiCloneFit

Reconstruct tree by SPhyR

Reconstruct tree by SPhyR

Comparison#

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

Comparing two trees by Ancestor-Descendent

Comparing two trees by Ancestor-Descendent

Comparing two trees by CASet

Comparing two trees by CASet

Comparing two trees by DISC

Comparing two trees by DISC

Comparing two trees by Different-Lineage

Comparing two trees by Different-Lineage

Comparing two trees by Genotype-Similarity

Comparing two trees by Genotype-Similarity

Comparing two trees by MLTD

Comparing two trees by MLTD

Comparing two trees by MP3

Comparing two trees by MP3

Comparing two trees by Robinson-Foulds

Comparing two trees by Robinson-Foulds

Comparing two trees by TPTED

Comparing two trees by TPTED

Assessment#

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

Reconstruct tree by Trisicell-PartF

Reconstruct tree by Trisicell-PartF

Visualization#

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

Visualizing a tree in clonal format

Visualizing a tree in clonal format

Visualizing a tree in dendrogram format

Visualizing a tree in dendrogram format

Gallery generated by Sphinx-Gallery