FISHtrees statistics

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Citations per year

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Popular tool citations

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Associated diseases

Associated diseases

FISHtrees specifications


Unique identifier OMICS_09042
Name FISHtrees
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Russell Schwartz <>

Publication for FISHtrees

FISHtrees in publications

PMCID: 5723949
PMID: 29279850
DOI: 10.1155/2017/5482750

[…] by taking advantage of information on tumor heterogeneity lost to prior microarray-based approaches on a set of fluorescent in situ hybridization (fish) data. chowdhury et al. [–] propose a software fishtrees to build evolutionary trees of single tumors with fish data. fishtrees models gain or loss of genetic regions at the scale of single genes, whole chromosomes, or the entire genome, […]

PMCID: 4117424
PMID: 25078894
DOI: 10.1371/journal.pcbi.1003740

[…] accuracy and in our ability to accurately classify tumors from their inferred evolutionary models. the newly developed algorithms have been released through our publicly available software, fishtrees., this is a plos computational biology methods article., in this paper, we develop new methods to advance the theory of phylogenetic inference for reconstructing evolutionary histories […]

PMCID: 3694640
PMID: 23812984
DOI: 10.1093/bioinformatics/btt205

[…] results in improved accuracy, relative to unstructured gene copy number data, at predicting tumor state and future metastasis., availability: source code for software that does fish tree building (fishtrees) and the data on cervical and breast cancer examined here are available at, contact: [email protected], supplementary information: […]

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FISHtrees institution(s)
Joint Carnegie Mellon/University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA; Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA; Computational Biology Branch, National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, MD, USA; Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, U.S. National Institutes of Health, Bethesda, MD, USA; Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
FISHtrees funding source(s)
This research was supported in part by the Intramural Research Program of the U.S. National Institutes of Health, National Cancer Institute, National Library of Medicine, and by U.S. National Institutes of Health grants 1R01CA140214 and 1R01AI076318.

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