Secator/DPC – Sequence Clustering from a Multiple Alignment

Secator/DPC

:: DESCRIPTION

The Secator program for clustering protein sequences or coordinates data with the Secator rule on the dendrogram of hierarchical clustering.

The DPC program for clustering protein sequences or coordinates data with the DPC rule (small density between two high densities) for selecting the number of clusters

::DEVELOPER

Nicolas Wicker

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

Secator/DPC

:: MORE INFORMATION

Citation

Secator: a program for inferring protein subfamilies from phylogenetic trees.
N.Wicker, G.R.Perrin, J.C.Thierry and O.Poch
Mol.Biol.Evol., 2001, 8:1435-1441

Density of points clustering, application to transcriptomics data analysis.
N.Wicker, D.Dembele, W.Raffelsberger and O.Poch
Nucleic Acids Res., 2002, 18:3992-4000

Typhon Beta – A Multiple Alignment Indexing Tool

Typhon Beta

:: DESCRIPTION

Typhon is an algorithm for building an index from a multiple alignment for use in seeding local alignments to a query sequence.

::DEVELOPER

Jason Flannick , Serafim Batzoglou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
GCC
Mandala

:: DOWNLOAD

Typhon

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2005 Aug 12;33(14):4563-77. Print 2005.
Using multiple alignments to improve seeded local alignment algorithms.
Flannick J, Batzoglou S.

ProAlign 0.5a3 – Probabilistic Multiple Alignment program

ProAlign 0.5a3

:: DESCRIPTION

ProAlign is a software implementing a multiple-alignment method that combines a Hidden Markov model (HMM), a progressive alignment algorithm, and a probabilistic character substitution model. Check below for much additional information.

::DEVELOPER

Michel C. Milinkovitch’s lab

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX / Linux / Windows
Java

:: DOWNLOAD

ProAlign

:: MORE INFORMATION

Citation

Ari Löytynoja and Michel C. Milinkovitch*
A hidden Markov model for progressive multiple alignment
Bioinformatics, 19:1505-1513 (2003)

StatSigMA beta / StatSigMA-w v2 – Computes P-value of (Whole-Genome) Multiple Alignment

StatSigMA beta / StatSigMA-w v2

:: DESCRIPTION

StatSigMA (Statistical Significance of Multiple Alignments) computes the statistical significance of multiple sequence alignments (of either nucleotide or amino acid sequences), much as BLAST’s E-values provide statistical significance for pairwise alignments.

StatSigMA-w (Statistical Significance of Whole-Genome Multiple Alignments),Given any multiple sequence alignment and a phylogeny of the aligned sequences, assesses the accuracy of the alignment and identifies suspiciously aligned regions.

::DEVELOPER

The Computational & Synthetic Biology group – COMPUTER SCIENCE & ENGINEERING at UNIVERSITY OF WASHINGTON

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Linux
GCC

:: DOWNLOAD

StatSigMA , StatSigMA-w

:: MORE INFORMATION

Citation:

A. Prakash, M. Tompa,
“Assessing the discordance of multiple sequence alignments“,
IEEE/ACM Trans Comput Biol Bioinform, vol. 6 (2009) 542-51.Pubmed 19875854.

X. Chen, M. Tompa,
“Comparative assessment of methods for aligning multiple genome sequences“,
Nat. Biotechnol., vol. 28 (2010) 567-72.

MLOGD – Detect Overlapping CDSs from Multiple Alignments

MLOGD

:: DESCRIPTION

MLOGD (Maximum Likelihood Overlapping Gene Detector) is a suite of software for detecting new protein-coding sequences (CDSs) by analysing the pattern of mutations across an input sequence alignment. In particular, the software can be used to detect new CDSs that overlap known CDSs in a different read-frame. Such CDSs can be difficult to detect with standard gene-finding algorithms (see below). The software is particularly useful for analysing virus genome alignments, where overlapping genes and ribosomal frameshifting sites are common.

::DEVELOPER

Andrew Firth

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
C++ Compiler
R Package
EMBOSS

:: DOWNLOAD

MLOGD

:: MORE INFORMATION

Citation

Firth A. E., Brown C. M., 2006,
Detecting Overlapping Coding Sequences in Virus Genomes,
BMC Bioinformatics, 7, 75.

MUMMALS 1.01 – MUltiple alignment with Multiple MAtch state models of Local Structure

MUMMALS 1.01

:: DESCRIPTION

MUMMALS constructs a multiple sequence alignment given a set of protein sequences.

::DEVELOPER

Grishin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

MUMMALS

:: MORE INFORMATION

Citation:

J. Pei and N.V.Grishin (2006)
“MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information“.
Nucleic Acids Res 34(16): 4364-4374

FAST 20070903 – Fourier Transform based Algorithms for Significance Testing of ungapped Multiple Alignments

FAST 20070903

:: DESCRIPTION

FAST (Fourier transform based Algorithms for Significance Testing of ungapped multiple alignments) is an open-source C/C++ package of programs and associated libraries for evaluating ungapped multiple alignments.

:: DEVELOPER

Uri Keich

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
C Compiler

:: DOWNLOAD

FAST

:: MORE INFORMATION

Citation:

Bioinformatics. 2008 Feb 15;24(4):577-8. Epub 2008 Jan 6.
FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments.
Nagarajan N, Keich U.

BOXSHADE 3.2.3 – Pretty Printing and Shading of Multiple-Alignment files

BOXSHADE 3.2.3

:: DESCRIPTION

Boxshade is a program for creating good looking printouts from multiple-aligned protein or DNA sequences.

::DEVELOPER

K. Hofmann and M. Baron.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

BOXSHADE

:: MORE INFORMATION

GERP++ 20110522 – Analyze Evolutionary Rates and Find Constrained Elements in a Multiple Alignment

GERP++ 20110522

:: DESCRIPTION

GERP++ (Genomic Evolutionary Rate Profiling) identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint.

::DEVELOPER

Sidow Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GERP++

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2010 Dec 2;6(12):e1001025.
Identifying a high fraction of the human genome to be under selective constraint using GERP++.
Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S.

codaln 1.0 / code2aln 1.2 – Progressive Multiple Alignments of Partially Coding Sequences.

codaln 1.0 / code2aln 1.2

:: DESCRIPTION

codaln is the successor of code2aln.codaln produces multiple nucleic acid alignments using information on coding and non-coding regions as part of the scoring function. This is done in order to prevent the problem of higher sequence divergency on the level of nucleic acids as compared to the underlying protein sequences in the case of coding at a certain region of the input nucleic acid sequences. The program allows plenty of user intervention to overrule the defaults.

::DEVELOPER

Bioinformatics Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

codaln , code2aln

:: MORE INFORMATION

Citation

Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences
Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler
BMC Bioinformatics 6: 160 [epub] (2005)