CHROMA 1.0 – Annotated Multiple Sequence Alignments

CHROMA 1.0

:: DESCRIPTION

CHROMA is a tool for generating annotated multiple sequence alignments in a convenient format for publication.CHROMA takes your aligned multiple sequence data, annotates residues according to a consensus and displays the alignment using different font formats (text and background colours, bold and italic).

::DEVELOPER

Llew Goodstadt

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux
MS Word

:: DOWNLOAD

CHROMA for win ; for Linux

:: MORE INFORMATION

Citation

Leo Goodstadt and Chris P. Ponting
CHROMA: consensus-based colouring of multiple alignments for publication.
Bioinformatics. 2001 Sep;17(9):845-6.

Align-m 2.3 – Multiple Sequence Alignment

Align-m 2.3

:: DESCRIPTION

Align-m is an accurate and highly versatile multiple alignment program. It consists of 3 modules, S2P, P2P and P2M (see figure, manual), which can be used separately or consecutively to accomplish several tasks
– Multiple sequence alignment
– Include extra information to guide the sequence alignment
– Multiple structure alignment
– Homology modeling by (iteratively) combining sequence and structure alignment data
– ‘Filtering’ of Blast or other pairwise alignments
– Combining many alignments into 1 consensus
– Multiple genome alignment (can cope with rearrangements)

::DEVELOPER

Vrije Universiteit Brussel – Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux

:: DOWNLOAD

Align-m

:: MORE INFORMATION

Citation

Van Walle I, Lasters I, Wyns L.
Align-m–a new algorithm for multiple alignment of highly divergent sequences.
Bioinformatics. 2004 Jun 12;20(9):1428-35. Epub 2004 Feb 12.

Laj 070222 – Alignment Viewer

Laj 070222

:: DESCRIPTION

Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and annotation links to other web sites containing additional information about particular regions.The program is written in Java in order to provide a graphical user interface that is portable across a variety of computer platforms; indeed its name stands for “Local Alignments with Java”. Currently it exists in two forms, a stand-alone application and a web-based applet, with slightly different capabilities.

::DEVELOPER

Cathy Riemer

:: SCREENSHOTS

:: REQUIREMENTS

Windows/ Linux / Mac OsX
JAVA

:: DOWNLOAD

Laj

:: MORE INFORMATION

Citation

Wilson MD, Riemer C, Martindale DW, Schnupf P, Boright AP, Cheung TL, Hardy DM, Schwartz S, Scherer SW, Tsui LC, Miller W, Koop BF.
Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5.
Nucleic Acids Res. 2001 Mar 15;29(6):1352-65.

Align 200807 – DNA Sequence Alignment Editor

Align 200807

:: DESCRIPTION

Align is a manual DNA sequence alignment editor.

::DEVELOPER

SequentiX – Digital DNA Processing

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

Align

:: MORE INFORMATION

Request a free trial license to use the full spectrum of features for one month and free of charge!

Se-Al 2.0a11 – Manual Sequence Alignment Editor

Se-Al 2.0a11

:: DESCRIPTION

Se-Al is an application for creating multiple sequence alignments from nucleotide and amino acid sequences. At the moment it does not do any automatic alignments but is intended for the production of hand alignments and for preparing input for alignment programs such as CLUSTAL and phylogeny reconstruction programs such as PHYLIP and PAUP. It is particularly useful for manipulating protein coding DNA/RNA sequences.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

:: REQUIREMENTS

MacOS

:: DOWNLOAD

Se-Al

:: MORE INFORMATION

Quasar 1.2 – Score & Rank Sequence-structure Alignments

Quasar 1.2

:: DESCRIPTION

Quasar (quality of sequence–structure alignments ranking) is a flexible tool for calculating quality scores of sequence-structure alignments. The main reason for its flexibility is that you do not have to write any additional Java code in order to combine single alignment quality scores (also called scoring schemes) to scoring function (done by score conductors) but you only have to provide the system a XML – like configuration file.

::DEVELOPER

Institut für Informatik, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

Quasar

:: MORE INFORMATION

Citation

Fabian Birzele, Jan Gewehr, Ralf Zimmer.
QUASAR–scoring and ranking of sequence-structure alignments.
Bioinformatics, vol 21, no. 24, pp. 4425–4426, Dec 2005.

MetaPAT 20070215 – Tool for the Alignment of Metabolic Pathways

MetaPAT 20070215

:: DESCRIPTION

MetaPAT is a tool for the alignment of metabolic pathways.MetaPAT aligns metabolic pathways based on the FIT-MATCH algorithm.METAPAT can also detect alignments which differ only very slightly from higher scoring ones and might thus not be of interest.

::DEVELOPER

Florian Rasche (m3rafl@minet.uni-jena.de)

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux

:: DOWNLOAD

MetaPAT for Linux ; for win

:: MORE INFORMATION

Citation

S. Wernicke and F. Rasche.
Simple and fast alignment of metabolic pathways by exploiting local diversity.
Bioinformatics (2007) 23 (15): 1978-1985

PicXAA 1.03 / PicXAA-R 1.0 – Probabilistic Maximum Accuracy Alignment / for RNA Structural Alignment

PicXAA 1.03 / PicXAA-R 1.0

:: DESCRIPTION

PicXAA is a probabilistic non-progressive alignment algorithm that finds protein multiple sequence alignments with maximum expected accuracy.

PicXAA-R is an extension of PicXAA for greedy structural alignment of NonCoding RNAs.

::DEVELOPER

Byung-Jun Yoon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

PicXAA / PicXAA-R

:: MORE INFORMATION

Citation

PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon,
Nucleic Acids Research, 38(15):4917-4928, 2010.

PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon,
BMC Bioinformatics, 12(Suppl 1):S38, 2011

SCALI – Non-sequential Structure-based Alignment

SCALI

:: DESCRIPTION

SCALI (Structural Core ALIgnment), can efficiently find conserved packing arrangements, even if they are non-sequentially ordered in space. SCALI alignments conserve remote sequence similarity and contain fewer alignment errors. Clustering of our pairwise non-sequential alignments shows that recurrent packing arrangements exist in topologically different structures. For example, the 3-layer sandwich domain architecture may be divided into four structural subclasses based on internal packing arrangements. These subclasses represent an intermediate level of structure classification, more general than topology but more specific than architecture as defined in CATH. A strategy is presented for developing a set of predictive hidden Markov models based on multiple SCALI alignments.

SCALI Online Version

::DEVELOPER

Chris Bystroff

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

SCALI

:: MORE INFORMATION

Citaiton

Yuan X & Bystroff, C. (2005)
Non-sequential Structure-based Alignments Reveal Topology-independent Core Packing Arrangements in Proteins.
Bioinformatics 27(7):1010-1019.

SRMA 0.1.15 – Sequence Re-alignment for Next Generation Sequencing

SRMA 0.1.15

:: DESCRIPTION

SRMA (Short Read Micro re-Aligner) is a software package that performs sequence re-alignment for next generation sequencing technology.It fixes artifacts introduced by aligning each read independently, significantly reducing the false positive detection, while cleaning insertions and deletions.

::DEVELOPER

Nils Homer

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

SRMA

:: MORE INFORMATION

Citation:

Homer N, Nelson SF.
Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA.
Genome Biol. 2010 Oct 8;11(10):R99 PMID: 20932289