Tag: Alignment-free

Spaced Words – Alignment-free Sequence Comparison

Spaced Words

:: DESCRIPTION

Spaced Words is a new approach to alignment-free sequence comparison. While most alignment-free algorithms compare the word-composition of sequences, Spaced Words uses a pattern of care and don’t care positions.

::DEVELOPER

Department of Bioinformatics ,  University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Spaced Words

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 3.
Fast alignment-free sequence comparison using spaced-word frequencies.
Leimeister CA1, Boden M, Horwege S, Lindner S, Morgenstern B.

CAFE 1.0 – aCcelerated Alignment-FrEe sequence analysis

CAFE 1.0

:: DESCRIPTION

CAFE is a standalone software for efficient calculation of 28 alignment-free dissimilarity measures.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

CAFE

:: MORE INFORMATION

Citation

Lu YY, Tang K, Ren J, Fuhrman JA, Waterman MS, Sun F.
CAFE: aCcelerated Alignment-FrEe sequence analysis.
Nucleic Acids Res. 2017 Jul 3;45(W1):W554-W559. doi: 10.1093/nar/gkx351. PMID: 28472388; PMCID: PMC5793812.

D2NGS – Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads

D2NGS

:: DESCRIPTION

D2NGS is a C++ package which is intended to implement a program for the alignment-free comparison of genome sequences using NGS data using d2, d2* and d2S.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 D2NGS

:: MORE INFORMATION

Citation

Song K, Ren J, Zhai ZY, Liu XM, Deng MH, and Sun FZ (2012)
Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads: Extended Abstract
Research in Computational Molecular Biology, 272-285.

QCluster – Extending Alignment-free Measures with Quality Values for Reads Clustering

QCluster

:: DESCRIPTION

Qcluster is a software of extending alignment-free measures with quality values for reads clustering.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 QCluster

:: MORE INFORMATION

Citation

Clustering of reads with alignment-free measures and quality values.
Comin M, Leoni A, Schimd M.
Algorithms Mol Biol. 2015 Jan 28;10:4. doi: 10.1186/s13015-014-0029-x

EP-sim – Multiple-resolution Alignment-free Measure based on Entropic Profiles

EP-sim

:: DESCRIPTION

EP-sim is a software of multiple-resolution alignment-free measure based on Entropic Profiles

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 EP-sim

:: MORE INFORMATION

Citation

On the comparison of regulatory sequences with multiple resolution Entropic Profiles.
Comin M, Antonello M.
BMC Bioinformatics. 2016 Mar 18;17(1):130. doi: 10.1186/s12859-016-0980-2.

UnderlyingApproach – Alignment-Free Phylogeny of Whole Genomes using Underlying Subwords

UnderlyingApproach

:: DESCRIPTION

The Underlying Approach (UA) builds a scoring function based on this set of patterns, called underlying. This set is by construction linear in the size of input, without overlaps, and can be efficiently constructed. Results show the validity of our method in the reconstruction of phylogenetic trees, where the Underlying Approach outperforms the current state of the art methods. Moreover, the accuracy of UA is achieved with a very small number of subwords, which in some cases carry meaningful biological information.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 UnderlyingApproach

:: MORE INFORMATION

Citation

Algorithms Mol Biol. 2012 Dec 6;7(1):34. doi: 10.1186/1748-7188-7-34.
Alignment-free phylogeny of whole genomes using underlying subwords.
Comin M, Verzotto D.

alfy 1.5 – Alignment-Free local homologY

alfy 1.5

:: DESCRIPTION

alfy is a computer program for comparing one or more query DNA sequences to a set of subject sequences. For each query sequence the output consists of a list of intervals indicating the closest homologue among the set of subject sequences.

::DEVELOPER

Bernhard Haubold

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • C Compiler

:: DOWNLOAD

 alfy

:: MORE INFORMATION

Citation

Alignment-free detection of local similarity among viral and bacterial genomes.
Domazet-Lošo M, Haubold B.
Bioinformatics. 2011 Jun 1;27(11):1466-72.

pim 0.3 – Alignment-free Estimation of Genetic Diversity

pim 0.3

:: DESCRIPTION

pim is a program for efficiently estimating the number of mismatches between a pair of unaligned sequences

::DEVELOPER

Bernhard Haubold

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • C Compiler

:: DOWNLOAD

 pim

:: MORE INFORMATION

Citation

B. Haubold, F. A. Reed, and P. Pfaffelhuber.
Alignment-free estimation of nucleotide diversity.
Bioinformatics, doi: 10.1093/bioinformatics/btq689, 2010.

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