Can I use the results of copykat to build phylogenetic tree?

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Assessment

Difficulty
5/5
Estimated time
Over a week
Newbie friendliness
20/100
Issue type
Feature
Clarity
Needs clarification
Activity status
Stale
Tech stack
r
Domain
bioinformatics

Research direction

The issue names no files, tests, or entry points. First determine whether copykat exposes copy-number states suitable for phylogenetic reconstruction; completion would require a documented, supported workflow or a clearly scoped implementation for building a tree from copykat results.

Written by the indexing model from the issue text.

Description

Dear developers,
I want to use CNV to build phylogenetic tree. In infercnv, they do HMM to predict copy state of region then do clonal evolution analysis. But in copykat it still is a cnv score. How to bulid phylogenetic tree based on the results of copykat? Can I do it use copykat?

Dominant language
R
Stars
305
Forks
66
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