ALFRED-G statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ALFRED-G
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Protocols

ALFRED-G specifications

Information


Unique identifier OMICS_19116
Name ALFRED-G
Alternative name ALFRED
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A set of n sequences.
Input format FASTA
Output data An n x n matrix of distance estimate for use in Phylogenetic inference.
Operating system Unix/Linux, Mac OS
Programming languages C++, Perl
Computer skills Advanced
Stability Stable
Requirements
A modern C++ ready compiler, cmake, Git
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Srinivas Aluru

Publications for ALFRED-G

ALFRED-G citations

 (4)
library_books

A Novel Method for Alignment free DNA Sequence Similarity Analysis Based on the Characterization of Complex Networks

2016
Evol Bioinform Online
PMCID: 5054945
PMID: 27746676
DOI: 10.4137/EBO.S40474

[…] dissimilarity between different species. Their approach preserves the physiochemical properties, positional information, and the codon usage bias of nucleotides. Recently, Thankachan et al. presented ALFRED, an alignment-free distance computation method, which solves the generalized common substring search problem via exact computation. Pizzi presented MissMax, an exact algorithm for the computati […]

call_split

Phylogeny Reconstruction with Alignment Free Method That Corrects for Horizontal Gene Transfer

2016
PLoS Comput Biol
PMCID: 4918981
PMID: 27336403
DOI: 10.1371/journal.pcbi.1004985
call_split See protocol

[…] counterparts (). We also calculated the distances to the Eisen-trees for trees built using other alignment-free methods, namely Average Common Substring (ACS), CVTree, D2, kmacs, and Spaced Words and ALFRED-G. These alternative methods were given both raw data and also a variety of filtered inputs.SlopeTree proved to be an effective tool for strain-level phylogeny, despite the number of matches be […]

library_books

Membrane guanylate cyclase, a multimodal transduction machine: history, present, and future directions

2014
PMCID: 4079103
PMID: 25071437
DOI: 10.3389/fnmol.2014.00056

[…] nto the production of the second messenger occurred in the cell's plasma membrane.The “cyclic AMP second messenger concept” was brought to the molecular level by the discoveries of Martin Rodbell and Alfred G. Gilman for which in 1994 they shared the Nobel Prize in physiology/medicine. They demonstrated that G-protein signaling bridged the gap between the hormonal signal and activation of the aden […]

library_books

Structural Aspects of GPCR G Protein Coupling

2013
PMCID: 3877993
PMID: 24386514
DOI: 10.5487/TR.2013.29.3.149

[…] In 1994, Alfred G. Gilman and Martin Rodbell were awarded the Nobel Prize in Physiology or Medicine for “their discovery of G-proteins and the role of these proteins in signal transduction in cells.” Eighteen […]


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ALFRED-G institution(s)
Department of Computer Science, University of Central Florida, Orlando FL, USA; Institute for Data Engineering and Science, Georgia Institute of Technology, Atlanta, GA, USA; School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA; School of Electrical Engineering and Computer Science, Louisiana State University, Baton Rouge, LA, USA
ALFRED-G funding source(s)
Supported by the U.S. National Science Foundation grant IIS-1416259 and the U.S. National Science Foundation grant IIS-1416259.

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