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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


No version available


  • person_outline Russell Schwartz

Publication for FISHtrees

FISHtrees citations


An Improved Binary Differential Evolution Algorithm to Infer Tumor Phylogenetic Trees

Biomed Res Int
PMCID: 5723949
PMID: 29279850
DOI: 10.1155/2017/5482750

[…] tree topology are branch, level, and edge. There are two features derived from data: (i) maximum copy number of each gene; (ii) average copy number of each gene. BDEP also compares with the published FISHtrees algorithm [], which is a state-of-the-art algorithm for phylogenetic tree based on FISH platform; the result is shown in . The experiment distinguishing primary from its corresponding metast […]


FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe

PLoS One
PMCID: 4928784
PMID: 27362268
DOI: 10.1371/journal.pone.0158569

[…] enetic methods that are designed to model species evolution and that are not necessarily suitable for cancer evolution (e.g., [, ]).In our recent work in this area, we implemented a software package, FISHtrees, to construct multi-scale models of single-cell FISH data, incorporating three types of copy number changes: single gene increases or decreases of one copy, single chromosome increases or de […]


Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics

PLoS Comput Biol
PMCID: 4117424
PMID: 25078894
DOI: 10.1371/journal.pcbi.1003740
call_split See protocol

[…] alving instead of doubling). The use of halving events is corrected heuristically by a procedure of subtree pruning and regrafting at line 24 of the pseudocode of Algorithm 3, described below, and in FISHtrees. We will produce the complete proof by deriving a series of lemmas for three cases that together will cover all possible and : […]


Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations

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

[…] iploid cells. For tree-based calculation of gene gain/loss, we measured the net gain or loss of each gene by the number of tree edges showing gain minus those showing loss over all trees generated by FISHtrees.We also performed a series of experiments on the use of progression tree statistics for classification tasks related to tumor progression and prognosis. In each case, we examined the use of […]


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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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