TwinCons – Alignment Score for detection of Ancient Homologies

TwinCons

:: DESCRIPTION

TwinCons is a software to detect noisy signals of deep ancestry of proteins or nucleic acids.

::DEVELOPER

The Williams Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

TwinCons

:: MORE INFORMATION

Citation

Penev PI, Alvarez-Carreño C, Smith E, Petrov AS, Williams LD.
TwinCons: Conservation score for uncovering deep sequence similarity and divergence.
PLoS Comput Biol. 2021 Oct 29;17(10):e1009541. doi: 10.1371/journal.pcbi.1009541. PMID: 34714829; PMCID: PMC8580257.

Minimap2 v2.23 – Pairwise Alignment for Nucleotide Sequences

Minimap2 v2.23

:: DESCRIPTION

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Minimap2

:: MORE INFORMATION

Citation

Li H.
New strategies to improve minimap2 alignment accuracy.
Bioinformatics. 2021 Oct 8:btab705. doi: 10.1093/bioinformatics/btab705. Epub ahead of print. PMID: 34623391.

Li H.
Minimap2: pairwise alignment for nucleotide sequences.
Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: 10.1093/bioinformatics/bty191. PMID: 29750242; PMCID: PMC6137996.

DiagAF 21.2.7 – Pre-Alignment Filter for Sequence Alignment

DiagAF 21.2.7

:: DESCRIPTION

DiagAF is a more accurate and efficient pre-alignment filter for sequence alignment. It can efficiently filter out candidates that contain errors greater than the edit distance threshold during read mapping.

::DEVELOPER

DiagAF team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

DiagAF

:: MORE INFORMATION

Citation

Yu C, Zhao Y, Zhao C, Ma H, Wang G.
DiagAF: A More Accurate and Efficient Pre-Alignment Filter for Sequence Alignment.
IEEE/ACM Trans Comput Biol Bioinform. 2021 Nov 17;PP. doi: 10.1109/TCBB.2021.3127879. Epub ahead of print. PMID: 34780330.

Seqotron v1.0.1 – Alignment Editor for Mac OS X

Seqotron v1.0.1

:: DESCRIPTION

Seqotron is a user-friendly sequence editor. It is written in Objective-C/Cocoa and runs on Mac OS X.

::DEVELOPER

Mathieu Fourment

 SCREENSHOTS

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

Seqotron

:: MORE INFORMATION

CitationFourment M, Holmes EC.
Seqotron: a user-friendly sequence editor for Mac OS X.
BMC Res Notes. 2016 Feb 17;9:106. doi: 10.1186/s13104-016-1927-4. PMID: 26887850; PMCID: PMC4756450.

 

Harvest 1.1.2 – A Suite of Core-genome Alignment and Visualization tools

Harvest 1.1.2

:: DESCRIPTION

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes. Harvest includes: Parsnp, a fast core-genome multi-aligner, Gingr, a dynamic visual platform, and harvest-tools, providing both a reference compressed binary archive and format conversion tools.

::DEVELOPER

The University of Maryland Center for Bioinformatics and Computational Biology (CBCB)

:: SCREENSHOTS

Harvest

:: REQUIREMENTS

  • Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 Harvest

:: MORE INFORMATION

Citation

Treangen TJ, Ondov BD, Koren S, Phillippy AM.
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.
Genome Biol. 2014;15(11):524. doi: 10.1186/s13059-014-0524-x. PMID: 25410596; PMCID: PMC4262987.

Topali 2.5 r3 – Statistical & Evolutionary Analysis of Multiple Sequence Alignments

Topali 2.5 r3

:: DESCRIPTION

Topali (tree TOPology-related analysis of ALignments Interface) is a software for statistical and evolutionary analysis of multiple sequence alignments.The extended TOPALi v2 provides phylogenetic model selection, Bayesian analysis (BA) and Maximum Likelihood (ML) phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysis.

::DEVELOPER

Information & Computational Sciences, The James Hutton Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 Topali

:: MORE INFORMATION

Citation

Milne I, Lindner D, Bayer M, Husmeier D, McGuire G, Marshall DF and Wright F (2008),
TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops,
Bioinformatics 25 (1), 126-127.

MUMmerGPU 2.0 – High-throughput sequence alignment using GPU

MUMmerGPU 2.0

:: DESCRIPTION

MUMmerGPU is an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs) in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA) from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies.

::DEVELOPER

Michael Schatz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • nVidia Card

:: DOWNLOAD

MUMmerGPU

:: MORE INFORMATION

MUMmerGPU is an open source project.

Citation:

Cole Trapnell and Michael C. Schatz
Optimizing data intensive GPGPU computations for DNA sequence alignment
Parallel Computing 2009 35(8-9)429-440

Spines 1.15 – C++ Software Package for Genomic Sequence Alignment and Analysis

Spines 1.15

:: DESCRIPTION

Spinesis a C++ software package for genomic sequence alignment and analysis.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

   Spines

:: MORE INFORMATION

Citation

Grabherr MG, Russell P, Meyer M, Mauceli E, Alfoldi J, Di Palma F, Lindblad-Toh K.
Genome-wide synteny through highly sensitive sequence alignment: Satsuma.
Bioinformatics. 2010 May 1;26(9):1145-51. Epub 2010 Mar 5

PAcAlCI 1.2 – Prediction of Accuracy in Alignments based on Computational Intelligence

PAcAlCI 1.2

:: DESCRIPTION

PAcAlCI  is novel intelligent algorithm based on least square support vector machine (LS-SVM) to predict how accurately ten different MSA tools could align a particular set of sequences.

::DEVELOPER

Francisco M. Ortuño Guzman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX /Windows
  • MatLab

:: DOWNLOAD

  PAcAlCI

 :: MORE INFORMATION

Citation

Ortuño, F.M., Valenzuela, O., Pomares, H., Rojas, F., Florido, J.P., Urquiza, J.M., Rojas, I.:
Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques.
Nucleic Acids Research 41, e26 (2013).

mVISTA – Compare Sequences & Visualize Alignments with Annotation Information

mVISTA

:: DESCRIPTION

mVISTA is a set of programs for comparing DNA sequences from two or more species up to megabases long and visualize these alignments with annotation information. mVISTA has a clean output, allowing for easy identification of sequence similarities and differences, and is easily configurable, enabling the visualization of alignments of various lengths at different levels of resolution. It is implemented as an on-line server that provides access to global pairwise, multiple and glocal (global with rearrangements) alignment tools.

mVISTA web version

::DEVELOPER

Genomics Division of Lawrence Berkeley National Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • JAVA

:: DOWNLOAD

mVISTA

:: MORE INFORMATION

mVISTA and Avid are free for academic or non-profit research institutions to use for internal research purposes. Commercial companies may submit sequences over the Web using the VISTA web site at no charge. To obtain a copy of mVISTA or Avid for internal use, commercial entities are required to purchase a site license for commercial use.

Citation:

Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9

Mayor C., Brudno M., Schwartz J. R., Poliakov A., Rubin E. M., Frazer K. A., Pachter L. S. and Dubchak I. (2000) VISTA: Visualizing Global DNA Sequence Alignments of Arbitrary Length. Bioinformatics, 16:1046.