Alignment-free Sequence Analysis Tools

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.

December 25, 2019
Preprint
Open Access

Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements

BioRxiv : the Preprint Server for Biology
Morteza HosseiniArmando J Pinho
July 31, 2019
Open Access

AluMine: alignment-free method for the discovery of polymorphic Alu element insertions

Mobile DNA
Tarmo PuurandMaido Remm
June 4, 2020
Open Access

Positional Correlation Natural Vector: A Novel Method for Genome Comparison

International Journal of Molecular Sciences
Lily HeStephen S-T Yau
October 21, 2019
Preprint
Open Access

Reference-free resolution of long-read metagenomic data

BioRxiv : the Preprint Server for Biology
Lusine KhachatryanJeroen F.J. Laros
March 7, 2019
Open Access

SNPs detection by eBWT positional clustering

Algorithms for Molecular Biology : AMB
Nicola PrezzaGiovanna Rosone
April 2, 2020
Open Access

IterCluster: a barcode clustering algorithm for long fragment read analysis

PeerJ
Jiancong WengRadoje Drmanac
March 6, 2019
Open Access

MetaMLP: A fast word embedding based classifier to profile target gene databases in metagenomic samples

BioRxiv : the Preprint Server for Biology
G. A. Arango-ArgotyL. Zhang
March 25, 2019
Open Access

AluMine: alignment-free method for the discovery of polymorphic Alu element insertions

BioRxiv : the Preprint Server for Biology
Tarmo PuurandMaido Remm
March 8, 2019

Alignment-free method for DNA sequence clustering using Fuzzy integral similarity

Scientific Reports
Ajay Kumar SawSoumyadeep Nandi
November 17, 2019

DL-CNV: A deep learning method for identifying copy number variations based on next generation target sequencing

Mathematical Biosciences and Engineering : MBE
Yun Xiang ZhangJi Dong Lang
February 21, 2020
Open Access

Whole-Genome k -mer Topic Modeling AssociatesBacterial Families

Genes
Ernesto Borrayo-CarbajalHugo Vélez-Pérez
March 13, 2020
Open Access

A strategy for predicting gene functions from genome and metagenome sequences on the basis of oligopeptide frequency distance

Genes & Genetic Systems
Takashi AbeToshimichi Ikemura
April 7, 2020
Preprint
Open Access

Genetic Distance Calculation Based on Locality Sensitive Hashing

BioRxiv : the Preprint Server for Biology
Gihan GamageI. Perera
May 27, 2020

CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning

Methods : a Companion to Methods in Enzymology
Jiayu Shang, Yanni Sun
June 30, 2020
Preprint
Open Access

Feature Frequency Profile-based phylogenies are inaccurate

BioRxiv : the Preprint Server for Biology
Y. LiAntonis Rokas
April 18, 2019
Open Access

Evolution of biosequence search algorithms: a brief survey

Bioinformatics
Gregory Kucherov

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