ALVIS 0.1 – Explorative Analysis and Visualisation of Multiple Sequence Alignments

ALVIS 0.1

:: DESCRIPTION

Alvis (Interactive non-aggregative multiple sequence ALignment VISualisation) is an open-source platform for the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its main visualisation method.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

ALVIS

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2016 May 5;44(8):e77. doi: 10.1093/nar/gkw022.
ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.
Schwarz RF, Tamuri AU, Kultys M, King J, Godwin J, Florescu AM, Schultz J, Goldman N.

PRANK 20170427 / webPRANK – Phylogeny-aware Progressive Sequence Alignment

PRANK 20170427

:: DESCRIPTION

PRANK (Probabilistic Alignment Kit) is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.

webPRANK is an easy-to-use web interface to the PRANK alignment algorithm.

::DEVELOPER

Löytynoja Lab, Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Windows

:: DOWNLOAD

 PRANK

:: MORE INFORMATION

Citation:

Phylogeny-aware alignment with PRANK.
Löytynoja A.
Methods Mol Biol. 2014;1079:155-70. doi: 10.1007/978-1-62703-646-7_10.

BMC Bioinformatics. 2010 Nov 26;11:579. doi: 10.1186/1471-2105-11-579.
webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.
Löytynoja A, Goldman N.

The effects of alignment error and alignment filtering on the sitewise detection of positive selection.
Jordan G, Goldman N.
Mol Biol Evol. 2012 Apr;29(4):1125-39. Epub 2011 Nov 1.

GenomeMapper 0.4.4 – Short Read Mapping tool

GenomeMapper 0.4.4

:: DESCRIPTION

GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference. If you are unsure which one is the appropriate GenomeMapper, you might want to use the latter.

:DEVELOPER

Dept. Weigel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 GenomeMapper

:: MORE INFORMATION

Citation

Genome Biol. 2009;10(9):R98. Epub 2009 Sep 17.
Simultaneous alignment of short reads against multiple genomes.
Schneeberger K, Hagmann J, Ossowski S, Warthmann N, Gesing S, Kohlbacher O, Weigel D.

PBSuite 150824 – Software for Long-Read Sequencing Data from PacBio

PBSuite 150824

:: DESCRIPTION

PBSuite includes:
PBJelly – the genome upgrading tool.
PBHoney – the structural variation discovery tool

PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles.

PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp).

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 PBSuite

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014 Jun 10;15:180. doi: 10.1186/1471-2105-15-180.
PBHoney: identifying genomic variants via long-read discordance and interrupted mapping.
English AC1, Salerno WJ, Reid JG.

English AC, Richards S, Han Y, Wang M, Vee V, et al. (2012)
Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology.
PLoS ONE 7(11): e47768. doi:10.1371/journal.pone.0047768

AMPS D2.3a – Alignment of Multiple Protein Sequences

AMPS D2.3a

:: DESCRIPTION

AMPS (Alignment of Multiple Protein Sequences) is a suite of programs for multiple sequence alignment. The programs include options to incorporate non-sequence information such as secondary structures. AMPS also implements flexible pattern matching and database scanning options.   AMPS includes functions for running randomisations to estimate the significance of sequence similarities.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AMPS

:: MORE INFORMATION

Citation:

Barton, G. J. (1990),
Protein Multiple Sequence Alignment and Flexible Pattern Matching“,
Meth. Enzymol., 183, 403-428.

Jalview 2.11.0 – Multiple Alignment Editor

Jalview 2.11.0

:: DESCRIPTION

Jalview is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

Jalview

:: MORE INFORMATION

Citation:

Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
Jalview Version 2 – a multiple sequence alignment editor and analysis workbench
Bioinformatics 25 (9) 1189-1191

STAMP 4.4.2 – Structural Alignment of Multiple Proteins

STAMP 4.4.2

:: DESCRIPTION

STAMP is a package for the alignment of protein sequences based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit’ superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments. It also provides a method for protein 3D structure data base scanning. In addition to structure comparison, the STAMP package provides input for programs to display and analyse protein sequence alignments and tertiary structures. Please note that, although STAMP outputs a sequence alignment, it is a program for 3D structures, and NOT sequences. If you are after a multiple sequence alignment for proteins of unknown 3D structure, stop reading now and contact GJB for information about AMPS, which can be used to perform multiple sequence alignments, or see www.jalview.org for GJB’s latest methods for this problem.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Window with Cygwin
  • GCC

:: DOWNLOAD

STAMP

:: MORE INFORMATION

Citation

Proteins. 1992 Oct;14(2):309-23.
Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels.
Russell RB1, Barton GJ.

ViroBLAST – BLAST web interface

ViroBLAST

:: DESCRIPTION

ViroBLAST is a BLAST web interface for nucleotide and amino acid sequence similarity searches.

ViroBLAST Online Version

::DEVELOPER

 Dr. Mullins Labat University of Washington

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • BLAST

:: DOWNLOAD

 ViroBLAST

:: MORE INFORMATION

Citation:

Deng W, Nickle DC, Learn GH, Maust B, and Mullins JI. 2007.
ViroBLAST: A stand-alone BLAST web server for flexible queries of multiple databases and user’s datasets.
Bioinformatics 23(17):2334-2336.

 

NanoOK 1.33 – Alignment and Analysis of Nanopore Reads

NanoOK 1.33

:: DESCRIPTION

NanoOK is a tool from TGAC for alignment and analysis of Nanopore reads. NanoOK will extract reads as FASTA or FASTQ files, align them (with a choice of alignment tools), then generate a comprehensive multi-page PDF report containing yield, accuracy and quality analysis.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / VirtualBox
  • Java

:: DOWNLOAD

  NanoOK

:: MORE INFORMATION

Citation:

NanoOK: Multi-reference alignment analysis of nanopore sequencing data, quality and error profiles.
Leggett RM, Heavens D, Caccamo M, Clark MD, Davey RP.
Bioinformatics. 2015 Sep 17. pii: btv540

MetaBinG 0.4 / MetaBinG2 – ultra-fast Metagenomic Sequence Classification system using GPUs

MetaBinG 0.4 / MetaBinG2

:: DESCRIPTION

MetaBinG  is an ultra-fast metagenomic sequence classification system using graphic processing units (GPUs).

MetaBinG2 is a fast and accurate metagenomic sequence classification system for samples with many unknown organisms

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MetaBinG / MetaBinG2

:: MORE INFORMATION

Citation:

Biol Direct. 2018 Aug 22;13(1):15. doi: 10.1186/s13062-018-0220-y.
MetaBinG2: a fast and accurate metagenomic sequence classification system for samples with many unknown organisms.
Qiao Y, Jia B, Hu Z, Sun C, Xiang Y, Wei C.

PLoS One. 2011;6(11):e25353. doi: 10.1371/journal.pone.0025353. Epub 2011 Nov 23.
MetaBinG: using GPUs to accelerate metagenomic sequence classification.
Jia P1, Xuan L, Liu L, Wei C.