PaPaRa 2.5 – PArsimony-based Phylogeny-Aware Read alignment program

PaPaRa 2.5

:: DESCRIPTION

PaPaRa is a PArsimony-based Phylogeny-Aware Read alignment program

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • C Compier

:: DOWNLOAD

 PaPaRa

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Aug 9;13:196. doi: 10.1186/1471-2105-13-196.
Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel.
Alachiotis N, Berger SA, Stamatakis A.

GapsMis 0.0.0 / GapMis 0.0.7 / GapMis-OMP 0.0.2 / libgapmis 0.0.9 – Pairwise Short-read Alignment

GapsMis 0.0.0 / GapMis 0.0.7 / GapMis-OMP 0.0.2 / libgapmis 0.0.9

:: DESCRIPTION

GapsMis is a tool for pairwise sequence alignment with a bounded number of gaps.

GapMis is a tool for pairwise sequence alignment with a single gap.

GapMis-OMP is the OpenMP-based version of GapMis.

libgapmis is an ultrafast library for pairwise short-read alignment, based on GapMis, including accelerated SSE-based and GPU-based versions.

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • EMBOSS
  • Python
  • C Compiler

:: DOWNLOAD

 GapsMisGapMis , GapMis-OMP , libgapmis 

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 11:S4. doi: 10.1186/1471-2105-14-S11-S4. Epub 2013 Nov 4.
libgapmis: extending short-read alignments.
Alachiotis N, Berger S, Flouri T, Pissis SP, Stamatakis A.

GapMis: a tool for pairwise sequence alignment with a single gap.
Flouri T, Frousios K, Iliopoulos CS, Park K, Pissis SP, Tischler G.
Recent Pat DNA Gene Seq. 2013 Aug;7(2):84-95.

Tomas Flouri, Kimon Frousios, Costas S. Iliopoulos, Kunsoo Park, Solon P. Pissis, and German Tischler.
Approximate string-matching with a single gap for sequence alignment.
In Proceedings of the Second ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), pp. 490-492, 2011. ACM Digital Library

MASon rev12 – Million Alignments in Seconds

MASon rev12

:: DESCRIPTION

MASon is a C++ library that uses high performance architectures to reduce the computing time of NGS analysis pipelines.

::DEVELOPER

the Center of Integrative Bioinformatics Vienna (CIBIV)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MASon

:: MORE INFORMATION

Citation

Rescheneder, P., von Haeseler, A., Sedlazeck, F. J.,
Mason: Million alignments in seconds,
In Proceedings of the International Conference on Bioinformatics: Models, Methods and Algorithms, 2012, Algarve, Portugal, accepted for publication

MatAlign V4A – Comparison, Alignment of PSSMs

MatAlign V4A

:: DESCRIPTION

MatAlign (Matrix Aligner) allows comparison among many matrices.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MatAlign

:: MORE INFORMATION

BioEdit 7.2.5 – Biological Sequence Alignment Editor

BioEdit 7.2.5

:: DESCRIPTION

BioEdit is a biological sequence alignment editor written for Windows 95/98/NT/2000/XP.  An intuitive multiple document interface with convenient features  makes alignment and manipulation  of sequences relatively easy on your desktop computer.    Several sequence manipulation and analysis options and links to external anaylsis programs facilitate a working environment which allows you to view and manipulate sequences with simple point-and-click operations.

::DEVELOPER

Tom Hall

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

BioEdit

:: MORE INFORMATION

MUMmer 4.0.0Beta2 / pymummer 0.11.0 – Alignment of Large-scale DNA & Protein Sequences

MUMmer 4.0.0Beta2/ pymummer 0.11.0

:: DESCRIPTION

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.

pymummer is Python3 module for running MUMmer and reading the output

::DEVELOPER

MUMmer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC / Python

:: DOWNLOAD

MUMmer, pymummer

:: MORE INFORMATION

MUMmer is now an open source project.

Citation:

MUMmer4: A fast and versatile genome alignment system
G. Marçais , A.L. Delcher, A.M. Phillippy, R. Coston, S.L. Salzberg, A. Zimin,
PLoS computational biology (2018), 14(1): e1005944.

seg-suite – Manipulate Segments and Alignments

seg-suite

:: DESCRIPTION

The seg suite provides tools for manipulating segments and alignments.

::DEVELOPER

Computational Biology Research Center (CBRC),

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 seg-suite

:: MORE INFORMATION

SPALN 2.3.3f – Mapping and Alignment of a set of cDNA Sequences onto a Genomic Sequence

SPALN 2.3.3f

:: DESCRIPTION

Spaln (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job. Spaln adopts multi-phase heuristics that makes it possible to perform the job on a conventional personal computer running under Unix/Linux with limited memory. The program is written in C++ and distributed as source codes and also as executables for a few platforms. Unless binaries are not provided, users must compile the program on their own system. Although the program has been tested only on a Linux operating system, it is likely to be portable to most Unix systems with little or no modifications. The accessory program sortgrcd sorts the gene loci found by spaln in the order of chromosomal position and orientation.

::DEVELOPER

Computational Biology Research Center (CBRC),

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 SPALN

:: MORE INFORMATION

Citation

Gotoh, O.
A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence
Nucleic Acids Research 36 (8) 2630-2638 (2008).

PROSTA-inter 20141229 – PROtein STructure Alignment tools

PROSTA-inter 20141229

:: DESCRIPTION

PROSTA-inter is a sequence-order independent alignment tool that automatically determines and aligns interaction interfaces
between two arbitrary types of complex structures (protein-protein, protein-DNA, and/or protein-RNA).

::DEVELOPER

Structural and Functional Bioinformatics Group, King Abdullah University of Science and Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

PROSTA-inter

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jun 15;31(12):i133-i141. doi: 10.1093/bioinformatics/btv242.
Finding optimal interaction interface alignments between biological complexes.
Cui X1, Naveed H1, Gao X

GraphCrunch 2.1.1 – Network Modeling, Alignment and Clustering

GraphCrunch 2.1.1

:: DESCRIPTION

GraphCrunch is a  software tool for network analysis, modeling and alignment. It automates tasks of finding the best fitting model for the network data, pairwise comparisons of networks, alignment of two networks using GRAAL algorithm (a better network alignment algorithm, MI-GRAAL, is also available for download), and provides capabilities of clustering network nodes based on their topological surrounding in the network.

::DEVELOPER

Nataša Pržulj, Imperial College

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • QT

:: DOWNLOAD

 GraphCrunch

:: MORE INFORMATION

Citation

GraphCrunch 2: Software tool for network modeling, alignment and clustering.
Kuchaiev O, Stevanović A, Hayes W, Pržulj N.
BMC Bioinformatics. 2011 Jan 19;12:24. doi: 10.1186/1471-2105-12-24.