Tag: Phylogen

TreeClone v1 – Reconstruction of Tumor Subclone Phylogeny Based on Mutation Pairs using Next Generation Sequencing Data

TreeClone v1

:: DESCRIPTION

TreeClone is a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution.

::DEVELOPER

Yuan Ji Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package

:: DOWNLOAD

TreeClone

:: MORE INFORMATION

Citation

[Submitted on 10 Mar 2017 (v1), last revised 25 Oct 2017 (this version, v2)]
TreeClone: Reconstruction of Tumor Subclone Phylogeny Based on Mutation Pairs using Next Generation Sequencing Data
Tianjian Zhou, Subhajit Sengupta, Peter Mueller, Yuan Ji

Phylogen 1.1 – Simulate Phylogenies

Phylogen 1.1

:: DESCRIPTION

Phylogen implements some straight-forward birth-death models for simulating phylogenies. It is intended to be fast and flexible and can simulate very large trees (depending on memory and speed of computer). It will then optionally reconstruct trees only containing extant lineages or produce trees containing a random sample of lineages. Trees can be written to a file for analysis in other packages. It will also draw lineages-through-time-plots.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Phylogen

:: MORE INFORMATION