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Protocols

RANGER-DTL specifications

Information


Unique identifier OMICS_08817
Name RANGER-DTL
Alternative name Rapid ANalysis of Gene family Evolution using Reconciliation-DTL
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A gene tree (rooted or unrooted) and a rooted species tree.
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Mukul S. Bansal
  • person_outline Manolis Kellis

Additional information


Previous version: http://compbio.mit.edu/ranger-dtl/

Publications for Rapid ANalysis of Gene family Evolution using Reconciliation-DTL

RANGER-DTL citations

 (9)
library_books

Horizontal gene transfer of Chlamydia: Novel insights from tree reconciliation

2018
PLoS One
PMCID: 5886423
PMID: 29621277
DOI: 10.1371/journal.pone.0195139

[…] HGTs in Chlamydiae, in order to improve the accuracy of the identification, we additionally evaluated the reliability of each potential candidate HGT events and mapping assignments using RAxML [] and RANGER-DTL 2.0 software package [].Tree reconciliation method is generally considered to be more powerful and sensitive in detecting HGT than distance-based methods [], but it is computationally inten […]

call_split

Function related replacement of bacterial siderophore pathways

2017
PMCID: 5776446
PMID: 28809850
DOI: 10.1038/ismej.2017.137
call_split See protocol

[…] Transfers were identified by species and gene tree reconciliation using the Ranger-DTL-D program () on ultrametric trees obtained from BEAST in addition to manual inspection (). […]

library_books

Toward a Metagenomic Understanding on the Bacterial Composition and Resistome in Hong Kong Banknotes

2017
Front Microbiol
PMCID: 5389987
PMID: 28450856
DOI: 10.3389/fmicb.2017.00632

[…] acquired from the HGTree database (Jeong et al., ). The gene family of an ARG was defined with the gene family with the highest proportion of valid hits (1e-5 and coverage > 50% in query or subject). RANGER-DTL (Bansal et al., ) was used for phylogenetic reconciliation analysis based on the gene tree and species tree provided by the HGTtree. The HGT rate in each family was calculated by dividing t […]

library_books

Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi

2017
PMCID: 5386878
PMID: 28235827
DOI: 10.1534/g3.116.038448

[…] taset could affect the results of SPRSupertrees, other types of phylogeny-based LGT detection software, including programs that accommodate paralogs, were also applied to the dataset. Notung (; ) and Ranger-DTL () use a parsimony analysis to infer duplications, losses, and transfers of genes within a phylogenetic tree. Using the default costs recommended by their authors (LGT score = 3), both meth […]

library_books

Towards sub quadratic time and space complexity solutions for the dated tree reconciliation problem

2016
PMCID: 4875752
PMID: 27213010
DOI: 10.1186/s13015-016-0077-5

[…] within a fixed period of time [, ].To date the fastest known approach for solving the dated tree reconciliation problem is Bansal et al.’s reconciliation algorithm, implemented in the software suite RANGER-DTL []. This O(n2logn) algorithm requires O(n2) space, offering a significant reduction from the initial solution proposed by Libeskind-Hadas and Charleston in 2009 (O(n7)) []. It is important […]

library_books

Concatenated alignments and the case of the disappearing tree

2014
BMC Evol Biol
PMCID: 4302582
PMID: 25547755
DOI: 10.1186/s12862-014-0266-0

[…] he fungi dataset. Full species names and additional taxonomic information are given in Additional files , , , and . To test for potential lateral gene transfer in our datasets we used PRUNIER [] and RANGER-DTL []. All 200 trees from the gammaproteobacteria data and the fungi data including 50 species were tested, respectively. Both programms require a reference tree, to which the single gene tree […]

Citations

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RANGER-DTL institution(s)
Department of Computer Science & Engineering, University of Connecticut, Storrs, CT, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
RANGER-DTL funding source(s)
Supported by NSF CAREER award IIS 1553421 and by NSF awards MCB 1616514 and IES 1615573, and by a University of Connecticut Summer Undergraduate Research Fund (SURF) award.

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