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.

AlignBucket – Identify Optimized Subsets of Protein Sequences for Alignment

AlignBucket

:: DESCRIPTION

AlignBucket is a software for splitting a fasta file into smaller pieces suitable for alignment with BLAST. The constraint used to optimize the result is the required minimum alignment coverage.

::DEVELOPER

Giuseppe Profiti , Piero Fariselli

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • g++

:: DOWNLOAD

 AlignBucket

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jul 30. pii: btv451.
AlignBucket: a tool to speed up ‘all-against-all’ protein sequence alignments optimizing length constraints.
Profiti G, Fariselli P, Casadio R

ParaAT 2.0 – Parallel Alignment & back-Translation

ParaAT 2.0

:: 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 National Genomics Data Center (NGDC)

:: 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.

PSMAlign – Progressive Stem Matching Alignment

PSMAlign

:: DESCRIPTION

PSMAlign is an open source tool that performs pairwise RNA secondary structures alignment based on the conserved stem pattern discovered. It enables alignment of large structures, such as those in the 23S ribosomal RNA family. Arbitrary pseudoknots are also allowed.

::DEVELOPER

Jimmy Ka Ho Chiu, Yi-Ping Phoebe Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Perl

:: DOWNLOAD

  PSMAlign

:: MORE INFORMATION

Citation

Pairwise RNA secondary structure alignment with conserved stem pattern.
Chiu JK, Chen YP.
Bioinformatics. 2015 Aug 13. pii: btv471.

CovaRNA / CovStat 1.16.0 – Detecting Long-range Covariations in Nucleotide Alignments

CovaRNA / CovStat 1.16.0

:: DESCRIPTION

CovaRNA / CovStat is a novel index-based computational method to detect long-range covariation on a genomic scale, as well as for determining the statistical significance of observed covariation patterns in alignment pairs.

::DEVELOPER

Shapiro Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C / R

:: DOWNLOAD

CovaRNA / CovStat 

:: MORE INFORMATION

Citation:

Bindewald E, Shapiro BA.
Computational detection of abundant long-range nucleotide covariation in Drosophila genomes.
RNA. 2013 Sep;19(9):1171-82. doi: 10.1261/rna.037630.112. Epub 2013 Jul 25. PMID: 23887147; PMCID: PMC3753924.

Alview 20160628 – Alignment View for BAM files

Alview 20160628

:: DESCRIPTION

Alview (Alignment Viewer) is a fast,portable tool for viewing short reads as native GUI program

:: DESCRIPTION

National Cancer Informatics Program

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/ MacOsX

:: DOWNLOAD

 Alview

:: MORE INFORMATION

Citation

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.
Finney RP, Chen QR, Nguyen CV, Hsu CH, Yan C, Hu Y, Abawi M, Bian X, Meerzaman DM.
Cancer Inform. 2015 Sep 13;14:105-7. doi: 10.4137/CIN.S26470.

ADAPT 1.00 – Alignment of DNA Associated Profiles Tool

ADAPT 1.00

:: DESCRIPTION

ADAPT (Alignment of DNA Associated Profiles Tool)

::DEVELOPER

BioInformatics Group Mittweida

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Java

:: DOWNLOAD

 ADAPT

:: MORE INFORMATION

Citation:

Bussiek M, Labudde D, Beier R, Mücke N, Nellen W:
“Correlation of bending propensity profiles at Dictyostelium discoideum promoters with developmental transcription regulation.” 2013

LocalAli – Local Alignment tool for Multiple Networks

LocalAli

:: DESCRIPTION

LocalAli is a fast and scalable local network alignment tool for the identification of functionally conserved modules in multiple networks.

::DEVELOPER

Jialu Hu ( jialu.hu@fu-berlin.de)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

LocalAli

:: MORE INFORMATION

Citation:

LocalAli: An Evolutionary-based Local Alignment Approach to Identify Functionally Conserved Modules in Multiple Networks.
Hu J, Reinert K.
Bioinformatics. 2014 Oct 4. pii: btu652.

NetCoffee – Alignment approach to Identify Functionally Conserved Proteins in Multiple Networks

NetCoffee

:: DESCRIPTION

NetCoffee is a fast and accurate algorithm which allows to find a global alignment of multiple protein-protein interaction networks.

::DEVELOPER

Jialu Hu ( jialu.hu@fu-berlin.de)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 NetCoffee

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Feb 15;30(4):540-8. doi: 10.1093/bioinformatics/btt715. Epub 2013 Dec 13.
NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks.
Hu J1, Kehr B, Reinert K.

CAB-align – Residue-residue Contact Area Based Alignment

CAB-align

:: DESCRIPTION

CAB-align (contact area-based alignment) is a flexible protein structure alignment method based on the residue-residue contact area.

::DEVELOPER

Takeda-Shitaka Lab (Laboratory of Biomolecular Design)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CAB-align

:: MORE INFORMATION

Citation

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.
Terashi G, Takeda-Shitaka M.
PLoS One. 2015 Oct 26;10(10):e0141440. doi: 10.1371/journal.pone.0141440.