Coval 1.5 – Improving the Quality of Short Read Alignment data

Coval 1.5

:: DESCRIPTION

Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads, thereby increasing the calling accuracy of currently available tools for SNP and indel identification.

::DEVELOPER

Coval team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl

:: DOWNLOAD

 Coval 

:: MORE INFORMATION

Citation

Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.
Kosugi S, Natsume S, Yoshida K, MacLean D, Cano L, Kamoun S, Terauchi R.
PLoS One. 2013 Oct 8;8(10):e75402. doi: 10.1371/journal.pone.0075402

Bio-samtools 2.6.2 – Ruby bindings for SAMtools

Bio-samtools 2.6.2

:: DESCRIPTION

Bio-samtools (bioruby-samtools) is a Ruby binding to the SAMtools library.Bio-samtools is a flexible and easy to use interface that programmers of many levels of experience can use to access information in the popular and common SAM/BAM format.

::DEVELOPER

Raoul J.P. Bonnal, Dan MacLean

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Ruby
  • BioRuby

:: DOWNLOAD

 Bio-samtools

:: MORE INFORMATION

Citation

bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby.
Etherington GJ, Ramirez-Gonzalez RH, MacLean D.
Bioinformatics. 2015 Mar 29. pii: btv178

Source Code Biol Med. 2012 May 28;7(1):6. doi: 10.1186/1751-0473-7-6.
Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments.
Ramirez-Gonzalez RH, Bonnal R, Caccamo M, Maclean D.

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.