ParaAT 1.0 – Parallel Alignment & back-Translation

ParaAT 1.0

:: DESCRIPTION

 ParaAT (Parallel Alignment and back-Translation) is a parallel tool that parallelly constructs protein-coding DNA alignments for a large number of homologs. ParaAT is well suited for large-scale data analysis in the high-throughput era, providing good scalability and exhibiting high parallel efficiency for computationally demanding tasks.

::DEVELOPER

The Zhang Lab — Computational Biology and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WIndows/ Linux / MacOsX
  • Perl

:: DOWNLOAD

  ParaAT

:: MORE INFORMATION

Citation

Biochem Biophys Res Commun. 2012 Mar 23;419(4):779-81. Epub 2012 Feb 27.
ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments.
Zhang Z, Xiao J, Wu J, Zhang H, Liu G, Wang X, Dai L.

PutGaps Beta – DNA Gapped File from Amino Acid Alignment

PutGaps Beta

:: DESCRIPTION

PutGaps is a software to add gaps to a DNA alignment file based on its Amino Acid equivalent.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

PutGaps

:: MORE INFORMATION

LiBis 0.1.5 – An Ultrasensitive Alignment method for low input Bisulfite Sequencing

LiBis 0.1.5

:: DESCRIPTION

LiBis is an integrated Python package for processing low input WGBS data such as cell-free DNA methylome and single-cell DNA methylome sequencing.

::DEVELOPER

Deqiang Sun Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • conda

:: DOWNLOAD

LiBis

:: MORE INFORMATION

ASH 1.2 / RASH / GASH – Alignment of Structural Homologs

ASH 1.2 / RASH / GASH

:: DESCRIPTION

ASH is a structure alignment program that has been developed for PDBj.

RASH Rapid ASH computes pair-wise alignments in under 1 second. RASH is generally sufficient if the structures are very similar.

GASH Genetic-algorithm ASH generates very accurate alignments in about twice the time as RASH. GASH is the best choice if the structures are only partially similar or if multiple solutions are required.

::DEVELOPER

ASH team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ASH

:: MORE INFORMATION

Citation

ASH structure alignment package: sensitivity and selectivity in domain classification.
Standley DM, Toh H, Nakamura H.
BMC Bioinformatics. 2007 Apr 4;8:116.

GASH: an improved algorithm for maximizing the number of equivalent residues between two protein structures.
Standley DM, Toh H, Nakamura H.
BMC Bioinformatics. 2005 Sep 8;6:221

Lalnview 3.0 – Graphical Viewer for Pairwise Sequence Alignments

Lalnview 3.0

:: DESCRIPTION

LalnView is a graphical program for visualizing local alignments between two sequences (protein or nucleic acids). Sequences are represented by colored rectangles to give an overall picture of the similarities between the two sequences. Blocks of similarity between the two sequences are colored according to the degree of identity between segments.

::DEVELOPER

Lauret Duret and Jean-Francois Gout.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 Lalnview

:: MORE INFORMATION

Citation

Duret, L., Gasteiger, E. and Perrière, G. (1996)
LalnView: a graphical viewer for pairwise sequence alignments.
Comput. Applic. Biosci., 12, 507-510

SibeliaZ 1.2.0 – Multiple Whole-genome Alignment based on de Bruijn graphs

SibeliaZ 1.2.0

:: DESCRIPTION

SibeliaZ is a whole-genome alignment and locally-coliinear blocks construction pipeline. The blocks coordinates are output in GFF format and the alignment is in MAF.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SibeliaZ

:: MORE INFORMATION

Citation:

Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ
Ilia Minkin, Paul Medvedev
bioRxiv 548123; doi: https://doi.org/10.1101/548123

CARNA 1.3.3 – Alignment of RNA Structure Ensembles

CARNA 1.3.3

:: DESCRIPTION

CARNA is a tool for multiple alignment of RNA molecules. CARNA requires only the RNA sequences as input and will compute base pair probability matrices and align the sequences based on their full ensembles of structures.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Dragos A. Sorescu, Mathias Moehl, Martin Mann, Rolf Backofen, and Sebastian Will
CARNA – alignment of RNA structure ensembles
Nucleic Acids Reseach, 40 no. W1 pp. W49-W53, 2012

SWIFT 1.0.1 / BALSAM 1.3 – Fast Local Alignment Searching

SWIFT 1.0.1 / BALSAM 1.3

:: DESCRIPTION

SWIFT suit is a software collection for fast index-based sequence comparison. It contains the following programs:

  • SWIFT — fast local alignment search, guaranteeing to find epsilon-matches between two sequences.
  • SWIFT BALSAM (BAsic fiLter for Semigobal non-gapped AlignMent search) — a very fast program to find semiglobal non-gapped alignments based on k-mer seeds.

::DEVELOPER

Wolfgang Gerlach ; Rasmussen KR, Stoye J, Myers EW.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / SUN solaris

:: DOWNLOAD

SWIFT ; BALSAM

:: MORE INFORMATION

Citation

K. Rasmussen, J. Stoye, E. W. Myers

Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length
In J. Comp. Biol. 13(2), 296-308, 2006.

ChromA 0.9 – Alignment for Chromatography Mass Spectrometry Data

ChromA 0.9

:: DESCRIPTION

ChromA (Chromatogram Alignment) provides the Dynamic Time Warping algorithm for the alignment of data from the domain of Gas- and Liquid-Chromatography Mass-Spectrometry. It uses additional constraints and can be configured to use different local functions to evaluate the similarity of mass spectra between chromatograms. It allows the definition of anchors, which are the positions of conserved compounds, constraining the alignment and providing a speedup. Furthermore, ChromA provides different visualizations of the alignment, as well as a textual format for further processing of chromatograms.

::DEVELOPER

Nils Hoffmann

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

ChromA

:: MORE INFORMATION

Citation

ChromA: Signal Based Retention Time Alignment for Chromatography-Mass Spectrometry Data
Nils Hoffmann; Jens Stoye
Bioinformatics 2009; doi: 10.1093/bioinformatics/btp343

GibbsCluster 2.0 – Simultaneous Alignment and Clustering of Peptide data

GibbsCluster 2.0

:: DESCRIPTION

GibbsCluster is a web server for simultaneous alignment and clustering of peptide data

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GibbsCluster

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 1;29(1):8-14. doi: 10.1093/bioinformatics/bts621. Epub 2012 Oct 24.
Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach.
Andreatta M1, Lund O, Nielsen M.