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.

AQUA 1.1 – Automatic Quality Improvment for Multiple Sequence Alignment

AQUA 1.1

:: DESCRIPTION

AQUA (Automated quality improvement for multiple sequence alignments)is a s implementation which relies on two alignment programs (MUSCLE and MAFFT), one refinement program (RASCAL) and one assessment program (NORMD)

::DEVELOPER

The Creevey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 AQUA

:: MORE INFORMATION

Citation

Muller J, Creevey CJ, Thompson JD, Arendt D, Bork P.
AQUA: automated quality improvement for multiple sequence alignments.
Bioinformatics. 2010 Jan 15;26(2):263-5. Epub 2009 Nov 19.

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

HoSeqI – Automated Homologous Sequence Identification in Gene Family Databases

HoSeqI

:: DESCRIPTION

HoSeqI (Homologous Sequence Identification) is a software environment allowing the automatic identification of homologous sequences and their classification into our comprehensive sequence family databases HOVERGEN and HOGENOM.

::DEVELOPER

PRABI-Doua

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

HoSeqI: automated homologous sequence identification in gene family databases.
Arigon AM, Perrière G, Gouy M.
Bioinformatics. 2006 Jul 15;22(14):1786-7.

HOMOLENS r5 – Homologous Sequences in Ensembl Animal Genomes

HOMOLENS r5

:: DESCRIPTION

HOMOLENS is a database of homologous genes from Ensembl organisms and Ensembl families, structured under ACNUC sequence database management system.

::DEVELOPER

Laboratoire de Biométrie et Biologie Evolutive

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Databases of homologous gene families for comparative genomics.
Penel S, Arigon AM, Dufayard JF, Sertier AS, Daubin V, Duret L, Gouy M, Perrière G.
BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S3. doi: 10.1186/1471-2105-10-S6-S3.

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

FSA 1.15.9 – Fast Statistical Alignment

FSA 1.15.9

:: DESCRIPTION

FSA (Fast Statistical Alignment) is a probabilistic multiple sequence alignment algorithm which uses a “distance-based” approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a phylogeny using only pairwise divergence estimates, FSA builds a multiple alignment using only pairwise estimations of homology. The program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multiple alignments which are accompanied by estimates of the alignment accuracy and uncertainty for every column and character of the alignment—previously available only with alignment programs which use computationally-expensive Markov Chain Monte Carlo approaches—yet can align thousands of long sequences.

::DEVELOPER

Robert Bradley Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FSA

:: MORE INFORMATION

Citation

Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L (2009)
Fast Statistical Alignment.
PLoS Computational Biology. 5:e1000392.

WOOF – Word-oriented Objective Function for Validation of Sequence Alignments

WOOF

:: DESCRIPTION

WOOF (Word-oriented objective function) is a method designed to rigourously apply the principle of visual alignment validation. WOOF does not actually make changes to a multiple sequence alignment, but is intead intended to choose the best alignment of a set of proteins from a set of such alignments that have been generated using different algorithms and parameter settings. The winning alignment is the one that best aligns a set of conserved patterns extracted using a pattern-finding approach such as TEIRESIAS. Patterns are weighted based on their statistical significance and position relative to other patterns.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Perl

:: DOWNLOAD

 WOOF

:: MORE INFORMATION

Citation

Beiko, R.G., Chan, C.X., and Ragan, M.A. (2005)
A word-oriented approach to alignment validation
Bioinformatics 21: 2230-2239

MAFFT 7.450 – Multiple Alignment Program

MAFFT 7.450

:: DESCRIPTION

MAFFT (Multiple sequence Alignment based on Fast Fourier Transform)is a multiple sequence alignment program for unix-like operating systems.  It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~10,000 sequences), etc.

MAFFT Server

::DEVELOPER

Computational Biology Research Center (CBRC),

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac OsX/ Linux

:: DOWNLOAD

MAFFT

:: MORE INFORMATION

Citation

Katoh, Rozewicki, Yamada 2019
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization
Briefings in Bioinformatics 20:1160-1166

Application of the MAFFT sequence alignment program to large data – reexamination of the usefulness of chained guide trees.
Yamada KD, Tomii K, Katoh K.
Bioinformatics. 2016 Jul 4. pii: btw412

Kazutaka Katoh and Hiroyuki Toh
Parallelization of the MAFFT multiple sequence alignment program
Bioinformatics (2010) 26 (15): 1899-1900