Tag: Alignment / BLAST

COCACOLA – Binning Metagenomic Contigs using Sequence COmposition, Read CoverAge, CO-alignment, and Paired-end Read LinkAge

COCACOLA

:: DESCRIPTION

COCACOLA is a general framework that combines different types of information: sequence COmposition, CoverAge across multiple samples, CO-alignment to reference genomes and paired-end reads LinkAge to automatically bin contigs into OTUs.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MatLab

:: DOWNLOAD

 COCACOLA

:: MORE INFORMATION

Citation

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge.
Lu YY, Chen T, Fuhrman JA, Sun F.
Bioinformatics. 2016 Jun 2. pii: btw290.

HAlign 2.1 – Fast Multiple Similar DNA/RNA Sequence Alignment

HAlign 2.1

:: DESCRIPTION

HAlign is a package of multi-platform Java software tools, which aimed at large scale multiple similar DNA/RNA sequence alignment. HAlign employs center star multiple sequence alignment strategy.

::DEVELOPER

Dr. Quan Zou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JRE
  • Hadoop

:: DOWNLOAD

 HAlign

:: MORE INFORMATION

Citation

HAlign: Fast Multiple Similar DNA/RNA Sequence Alignment Based on the Centre Star Strategy.
Zou Q, Hu Q, Guo M, Wang G.
Bioinformatics. 2015 Mar 25. pii: btv177.

BWBBLE – Short Read Alignment with Populations of Genomes

BWBBLE

:: DESCRIPTION

BWBBLE performs short-read alignment to a population of genomes represented by a reference multi-genome.

::DEVELOPER

Serafim’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • C Compiler

:: DOWNLOAD

 BWBBLE

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):i361-70. doi: 10.1093/bioinformatics/btt215.
Short read alignment with populations of genomes.
Huang L, Popic V, Batzoglou S.

ZORRO – Probabilistic Alignment Masking program

ZORRO

:: DESCRIPTION

ZORRO is a probabilistic masking program that accounts for uncertainty in protein sequence alignments. It assigns a confidence score to each column in the alignment that can be used for alignment masking and trimming.

::DEVELOPER

Jonathan A. Eisen’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX

:: DOWNLOAD

  ZORRO

:: MORE INFORMATION

Citation

PLoS One. 2012;7(1):e30288. doi: 10.1371/journal.pone.0030288. Epub 2012 Jan 17.
Accounting for alignment uncertainty in phylogenomics.
Wu M1, Chatterji S, Eisen JA.

WeaveAlign v1.2.1 – Multiple Sequence analysis in the presence Alignment uncertainty, using directed Acyclic Graphs

WeaveAlign v1.2.1

:: DESCRIPTION

WeaveAlign is a framework for combining a collection of multiple sequence alignments into a directed acyclic graph (DAG) structure, so as to permit efficient inference on very large sets of possible alignments.

::DEVELOPER

WeaveAlign team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

 WeaveAlign

:: MORE INFORMATION

Citation

Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs.
Herman JL, Novák Á, Lyngsø R, Szabó A, Miklós I, Hein J.
BMC Bioinformatics. 2015 Apr 1;16(1):108.

SFESA – Shift to Fix secondary structure ElementS in Alignments

SFESA

:: DESCRIPTION

SFESA is a tool to refine pairwise protein sequence alignment, with a combination of sequence and structural scoring by locally shifting secondary structure elements

::DEVELOPER

Grishin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SFESA

:: MORE INFORMATION

Citation:

Proteins. 2015 Mar;83(3):411-27. doi: 10.1002/prot.24746. Epub 2015 Jan 13.
Refinement by shifting secondary structure elements improves sequence alignments.
Tong J1, Pei J, Otwinowski Z, Grishin NV.

DISSECT 1.0.2 – Transcriptome-to-Genome Alignment Tool

DISSECT 1.0.2

:: DESCRIPTION

Dissect (DIScovery of Structural Alteration Event Containing Transcripts) is a transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. Dissect is suitable for whole transcriptome structural variation discovery problems involving sufficiently long reads or accurately assembled contigs.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  DISSECT

:: MORE INFORMATION

Citation

Yorukoglu D, Hach F, Swanson L, Collins CC, Birol I, Sahinalp SC
Dissect: detection and characterization of novel structural alterations in transcribed sequences
Bioinformatics. 2012 Jun 15;28(12):i179-87

CYNTENATOR 20101005 – Progressive Gene Order Alignment of 17 Vertebrate Genomes

CYNTENATOR 20101005

:: DESCRIPTION

CYNTENATOR is a progressive gene order alignment software to identify genomic regions of conserved synteny over a large set of diverging species. CYNTENATOR does not depend on nucleotide-level alignments and a priori homology assignment.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CYNTENATOR

:: MORE INFORMATION

Citation:

PLoS One. 2010 Jan 28;5(1):e8861.
CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes.
Rödelsperger  C, Dieterich C.

SHiAT 1.1 – Generates Plots of Variation along Sequence Alignment

SHiAT 1.1

:: DESCRIPTION

SHiAT (Shannon Heterogeneity in Alignments Tool) provides an intuitive graphical interface for the simultaneous calculation of three measures of sitewise variation in DNA or RNA alignments. The Shannon Information index, Hamming distance and (1-consensus frequency) are all calculated and displayed in a series of graphical plots. Multiple alignments may be imported and compared, and a data view panel allows easy copy-and-pasting into external applications.

::DEVELOPER

Joe Parker

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

SHiAT

:: MORE INFORMATION

BAli-Phy 3.6.0 – Bayesian Alignment and Phylogeny estimation

BAli-Phy 3.6.0

:: DESCRIPTION

BAli-Phy is MCMC software for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters).BAli-Phy can estimate phylogenetic trees from sequence data when the alignment is uncertain. Instead of conditioning on a single alignment estimate, BAli-Phy accounts for alignment uncertainty by integrating over all alignments. BAli-Phy does not rely on a guide tree because the alignment and the tree are co-estimated. Therefore it can construct phylogeny estimates of widely divergent sequences without bias toward a guide tree.

::DEVELOPER

BAli-Phy team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows

:: DOWNLOAD

 BAli-Phy

:: MORE INFORMATION

Citation

Suchard MA and Redelings BD
BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny,
Bioinformatics, 22:2047-2048, 2006.