AncesTree protocols

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AncesTree specifications

Information


Unique identifier OMICS_08946
Name AncesTree
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Requirements
CMake, Boost, LEMON, CPLEX
Maintained Yes

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Documentation


Maintainer


  • person_outline Benjamin Raphael <>

Publication for AncesTree

AncesTree in pipeline

2016
PMCID: 4823825
PMID: 27048880
DOI: 10.1038/ncomms11185

[…] a gene on chromosome x ref′=ref × 2+alt, alt′=alt; in case of copy neutral loh ref′=ref+alt/2 and alt′=alt/2. the reconstructed trees were redrawn in graphviz by using in-house scripts adapted from ancestree to show the trajectories of mutations with contribution ⩾0.05., we aligned rnaseq data from dipg3-pons 1 and dipg3-pons 2 (rna extraction and sequencing protocol described before) using […]


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AncesTree in publications

 (2)
PMCID: 5290319
PMID: 28139641
DOI: 10.1038/ncomms14114

[…] therefore works extremely well among metastases but is not applicable for liquid cancers. on the contrary, tools like phylowgs work extremely well in liquid cancers. last, we compared our results to ancestree, which roughly identified the evolutionarily related samples in pam03 but excluded 70% (63/90) of the variants (among them the driver gene mutations in kras and atm) in the inferred […]

PMCID: 4823825
PMID: 27048880
DOI: 10.1038/ncomms11185

[…] a gene on chromosome x ref′=ref × 2+alt, alt′=alt; in case of copy neutral loh ref′=ref+alt/2 and alt′=alt/2. the reconstructed trees were redrawn in graphviz by using in-house scripts adapted from ancestree to show the trajectories of mutations with contribution ⩾0.05., we aligned rnaseq data from dipg3-pons 1 and dipg3-pons 2 (rna extraction and sequencing protocol described before) using […]


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AncesTree institution(s)
Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI, USA

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