Tag: Sequence Aligner

DIAMOND v2.0.12 / AC-DIAMOND v1.0 – Accelerated BLAST compatible local Sequence Aligner

DIAMOND v2.0.12 / AC-DIAMOND v1.0

:: DESCRIPTION

DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.

AC-DIAMOND attempts to speed up DIAMOND via better SIMD parallelization and compressed indexing.

::DEVELOPER

the Algorithms in Bioinformatics lab. / Huijun Mai

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

DIAMOND , AC-DIAMOND

:: MORE INFORMATION

Citation

Buchfink B, Xie C, Huson DH.
Fast and sensitive protein alignment using DIAMOND.
Nat Methods. 2015 Jan;12(1):59-60. doi: 10.1038/nmeth.3176. Epub 2014 Nov 17. PMID: 25402007.

Mai H, Zhang Y, Li D, Leung HC, Luo R, Wong CK, Ting HF, Lam TW.
AC-DIAMOND v1: accelerating large-scale DNA-protein alignment.
Bioinformatics. 2018 Nov 1;34(21):3744-3746. doi: 10.1093/bioinformatics/bty391. PMID: 29771282.

LRD aligner – Rank-Based Sequence Aligners

LRD aligner

:: DESCRIPTION

LRD aligner (Local Rank Distance) is a rank-based sequence aligners

::DEVELOPER

Radu Ionescu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java
  • C++ Compiler

:: DOWNLOAD

 LRD aligner

:: MORE INFORMATION

Citation

A rank-based sequence aligner with applications in phylogenetic analysis.
Dinu LP, Ionescu RT, Tomescu AI.
PLoS One. 2014 Aug 18;9(8):e104006. doi: 10.1371/journal.pone.0104006

Cola a1 – Modular and Configurable Optimal Sequence Aligner

Cola a1

:: DESCRIPTION

Cola consists of an efficient implementation of a collection of sequence alignment algorithms, extending the Smith-Waterman and Smith-Waterman-Gap-Affine methods by the ability to apply a scoring function that is an arbitrary function of the size of consecutive nucleotide matches.

::DEVELOPER

Grabherr Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 Cola

:: MORE INFORMATION

Citation

Source Code Biol Med. 2014 Jun 9;9:12. doi: 10.1186/1751-0473-9-12. eCollection 2014.
Modular and configurable optimal sequence alignment software: Cola.
Zamani N1, Sundström G1, Höppner MP1, Grabherr MG