Multiple sequence alignment (MSA) is a key component in almost every comparative analysis of biological sequences (DNA or proteins). Moreover, MSA reconstruction is often the first step in bioinformatic pipelines, where MSA is later used for further analyses. Source text: Sela…
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Clustal Omega Clustal Omega

Clustal Omega

A package for making multiple sequence alignments of amino acid or nucleotide…

A package for making multiple sequence alignments of amino acid or nucleotide sequences, quickly and accurately. Clustal Omega can deal with very large numbers (many tens of thousands) of DNA/RNA or…

Protein Reference… Protein Reference Alignment Benchmark

PREFAB Protein Reference Alignment Benchmark

A database designed for testing multiple sequence alignment methods.

A database designed for testing multiple sequence alignment methods.

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DIALIGN DIALIGN

DIALIGN

A software tool for multiple sequence alignment by combining global and local…

A software tool for multiple sequence alignment by combining global and local alignment features. DIALIGN composes multiple alignments from local pairwise sequence similarities. This approach is…

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MUltiple Sequence… MUltiple Sequence Comparison by Log- Expectation

MUSCLE MUltiple Sequence Comparison by Log- Expectation

A computer program for creating multiple alignments of protein sequences.…

A computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile…

HAlign HAlign

HAlign

A package of multi-platform Java software tools, which aimed at large scale…

A package of multi-platform Java software tools, which aimed at large scale multiple similar DNA/RNA sequence alignment. HAlign employs center star multiple sequence alignment strategy. The input…

Web app
MAFFT MAFFT

MAFFT

A popular multiple sequence alignment (MSA) program with various options for…

A popular multiple sequence alignment (MSA) program with various options for the progressive method, the iterative refinement method and other methods. MAFFT version 7 has several new features,…

BAliBASE BAliBASE

BAliBASE

Provides high quality, manually refined, reference alignments based on 3D…

Provides high quality, manually refined, reference alignments based on 3D structural superpositions.

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eProbalign eProbalign

eProbalign

Computes maximal expected accuracy multiple sequence alignments from partition…

Computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities.

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muliAlignFree muliAlignFree

muliAlignFree

This R package is intended to implement a program for multiple alignment-free…

This R package is intended to implement a program for multiple alignment-free sequence comparison based on long genome sequence or NGS data. The multiple alignment-free statistics are more sensitive…

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Tree-based… Tree-based consistency objective function for…

T-Coffee Tree-based consistency objective function for alignment evaluation

A versatile multiple sequence alignment (MSA) method suitable for aligning…

A versatile multiple sequence alignment (MSA) method suitable for aligning virtually any type of biological sequences. T-Coffee provides more than a simple sequence aligner; rather it is a framework…

Desktop app
EDNA EDNA

EDNA

Multiple Sequence Alignment for Transcription Factor Binding Sites using Di…

Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution…

Desktop app
Phylo-Node Phylo-Node

Phylo-Node

A scalable toolkit that allows the user to go from sequence retrieval to…

A scalable toolkit that allows the user to go from sequence retrieval to phylogeny reconstruction. Phylo-Node can execute the analysis and process the resulting outputs from a suite of software…

Desktop app
Séance Séance

Séance

A community analysis pipeline for the 18S rRNA marker gene incorporating…

A community analysis pipeline for the 18S rRNA marker gene incorporating homopolymer modelling for clustering 454 data, phylogenetic placement and visualisation. Séance combines the alignment…

Desktop app
Sequence VARiability… Sequence VARiability Analysis Program

SVARAP Sequence VARiability Analysis Program

A tool to analyse the variability along multiple nucleotide sequences…

A tool to analyse the variability along multiple nucleotide sequences alignments. SVARAP calculates along the whole alignment the mean variability for a sliding window of 25 nucleotides. It combines…

Desktop app
BAli-Phy BAli-Phy

BAli-Phy BAli-Phy

A Bayesian posterior sampler that employs Markov chain Monte Carlo to explore…

A Bayesian posterior sampler that employs Markov chain Monte Carlo to explore the joint space of alignment and phylogeny given molecular sequence data. Simultaneous estimation eliminates bias toward…

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LocARNA LocARNA

LocARNA

A software for multiple alignment of RNA molecules. LOCARNA performs…

A software for multiple alignment of RNA molecules. LOCARNA performs Sankoff-style simultaneous alignment and folding. It only needs RNA sequences, which can be completed by structural information.…

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Kalign Kalign

Kalign

Improves both the accuracy and speed of multiple sequence alignment by…

Improves both the accuracy and speed of multiple sequence alignment by employing the Wu-Manber string-matching algorithm. Kalign follows a strategy analogous to the standard progressive method for…

Desktop app
Mugsy Mugsy

Mugsy

A multiple alignment tool for whole genomes. Mugsy uses Nucmer for pairwise…

A multiple alignment tool for whole genomes. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive…

Desktop app
Sequence-aligning… Sequence-aligning INnovative and Interactive…

SinicView Sequence-aligning INnovative and Interactive Comparison VIEWer

Allows the user to efficiently compare and evaluate assorted nucleotide…

Allows the user to efficiently compare and evaluate assorted nucleotide alignment results obtained by different tools. SinicView calculates similarity of the alignment outputs under a fixed window…

Desktop app
REDHORSE REDHORSE

REDHORSE

Uses genomic alignments, extracts genetic markers, and generates multiple…

Uses genomic alignments, extracts genetic markers, and generates multiple sequence alignments that can be used as input to existing recombination detection algorithms. REDHORSE implements a custom…

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AlignStat AlignStat

AlignStat

Aligns two alternative multiple sequence alignments to one another and…

Aligns two alternative multiple sequence alignments to one another and assessing their similarity. AlignStat enables the easy one-off online use of MSA similarity comparisons or into R pipelines. It…

Desktop app
HandAlign HandAlign

HandAlign

Bayesian reconstruction of phylogenetic history. HandAlign implements a…

Bayesian reconstruction of phylogenetic history. HandAlign implements a Bayesian model of sequence phylogeny with separate substitution and indel components. To perform inference of unknown variables…

Desktop app
Partial Order… Partial Order Alignment

POA Partial Order Alignment

A fast program for multiple sequence alignment (MSA) in bioinformatics. POA…

A fast program for multiple sequence alignment (MSA) in bioinformatics. POA guarantees that the optimal alignment of each new sequence versus each sequence in the MSA will be considered. Moreover,…

Desktop app
Historian Historian

Historian

A multiple aligner that aims at providing accurate historical reconstructions…

A multiple aligner that aims at providing accurate historical reconstructions of the evolution of a set of DNA or protein sequences. Historian uses an explicit evolutionary model of indel and…

Desktop app
GenNon-h GenNon-h

GenNon-h

Generates DNA multiple sequence alignments on a given phylogenetic tree.…

Generates DNA multiple sequence alignments on a given phylogenetic tree. GenNon-h provides the user with the nonstationary or nonhomogeneous phylogenetic data that is well suited for testing complex…

Desktop app
EvalMSA EvalMSA

EvalMSA

A software tool for evaluating and detecting outliers in multiple sequence…

A software tool for evaluating and detecting outliers in multiple sequence alignments (MSAs). EvalMSA allows the identification of divergent sequences in MSAs by scoring the contribution of each row…

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Pairagon Pairagon

Pairagon

A pair hidden Markov model (pair-HMM) based cDNA-to-genome alignment program.…

A pair hidden Markov model (pair-HMM) based cDNA-to-genome alignment program. Pairagon program can be used for both high- and low-identity sequences. By building a more realistic probabilistic model…

Desktop app
BAse COmposition… BAse COmposition CAlculator

BaCoCa BAse COmposition CAlculator

A package to identify biases in aligned sequence data which potentially mislead…

A package to identify biases in aligned sequence data which potentially mislead phylogenetic reconstructions. BaCoCa allows a parallel determination of a suite of different statistical properties of…

Desktop app
PRANK PRANK

PRANK

A probabilistic multiple alignment program for DNA, codon and amino-acid…

A probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK makes use of phylogenetic information to distinguish alignment gaps caused by insertions or deletions and,…

Desktop app
PAGAN PAGAN

PAGAN

A method for phylogeny-aware alignment of partial-order sequence graphs. PAGAN…

A method for phylogeny-aware alignment of partial-order sequence graphs. PAGAN infers ancestral sequences for the reference alignment and adds new sequences in their phylogenetic context, either to…

Desktop app
Web app
webPRANK webPRANK

webPRANK

Provides an easy-to-use interface to the PRANK phylogeny-aware alignment…

Provides an easy-to-use interface to the PRANK phylogeny-aware alignment algorithm. The webPRANK server supports the alignment of DNA, protein and codon sequences as well as protein-translated…

Desktop app
CUDAMPF CUDAMPF

CUDAMPF

A hardware-aware parallel framework for accelerating computational hotspots…

A hardware-aware parallel framework for accelerating computational hotspots within the hmmsearch pipeline as well as other sequence alignment applications. CUDAMPF achieves significant speedup by…

Desktop app
Ultra-large… Ultra-large alignments using Phylogeny-aware…

UPP Ultra-large alignments using Phylogeny-aware Profiles

Addresses the problem of alignment of very large datasets, potentially…

Addresses the problem of alignment of very large datasets, potentially containing fragmentary data. UPP can align datasets with up to 1,000,000 sequences. UPP produces highly accurate alignments for…

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MACSE: Multiple… MACSE: Multiple Alignment of Coding SEquences

MACSE MACSE: Multiple Alignment of Coding SEquences

A wide range of molecular analyses relies on multiple sequence alignments…

A wide range of molecular analyses relies on multiple sequence alignments (MSA). Until now the most efficient solution to align nucleotide (NT) sequences containing open reading frames was to use…

Desktop app
multiple sequence… multiple sequence alignment

msa multiple sequence alignment

Provides a unified R interface to the popular multiple sequence alignment…

Provides a unified R interface to the popular multiple sequence alignment algorithms ClustalW, ClustalOmega, and MUSCLE. msa requires no additional software and runs on all major platforms. Moreover,…

Web app
CorreLogo CorreLogo

CorreLogo

Generates a 3D representation of properties of user-submitted RNA or DNA…

Generates a 3D representation of properties of user-submitted RNA or DNA alignments. The visualized properties are information of single alignment columns, mutual information of two alignment…

Desktop app
WeaveAlign WeaveAlign

WeaveAlign

A framework for representing a set of sampled alignments as a directed acyclic…

A framework for representing a set of sampled alignments as a directed acyclic graph (DAG) whose nodes are alignment columns; each path through this DAG then represents a valid alignment. Since the…

Desktop app
SPARSE SPARSE

SPARSE

A simultaneous alignment and folding algorithm with a quadratic low complexity…

A simultaneous alignment and folding algorithm with a quadratic low complexity equivalent to a sequence alignment algorithm. SPARSE runs in quadratic time without sequence-based heuristics. To…

Web app
MSA-PAD MSA-PAD

MSA-PAD

A DNA multiple sequence alignment framework that uses PFAM protein domain…

A DNA multiple sequence alignment framework that uses PFAM protein domain information to align DNA sequences encoding either single or multiple protein domains. MSA-PAD has two alignment options:…

Web app
GenomeCons GenomeCons

GenomeCons

A web server for manipulating multiple genome sequence alignments and their…

A web server for manipulating multiple genome sequence alignments and their consensus sequences for high-throughput genome sequence analyses. This server facilitates the visual inspection of multiple…

Desktop app
MafFilter MafFilter

MafFilter

A command-line driven program written in C++ that enables the processing of…

A command-line driven program written in C++ that enables the processing of genome alignments stored in the Multiple Alignment Format in an efficient and extensible manner. MafFilter provides an…

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CodonLogo CodonLogo

CodonLogo

A tool for visualization of conserved codon patterns in multiple sequence…

A tool for visualization of conserved codon patterns in multiple sequence alignments. It can discriminate patterns of codon conservation from patterns of nucleotide conservation that appear…

Desktop app
Sequence Bundles Sequence Bundles

Sequence Bundles

A data visualisation method for representing multiple sequence alignments…

A data visualisation method for representing multiple sequence alignments (MSAs). It can aid in generating new insight and hypothesis making.

Desktop app
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GramAlign GramAlign

GramAlign

A time-efficient progressive Multiple Sequence Alignment (MSA) algorithm.

A time-efficient progressive Multiple Sequence Alignment (MSA) algorithm.

Desktop app
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PicXAA PicXAA

PicXAA

A probabilistic nonprogressive alignment algorithm that finds protein (or DNA)…

A probabilistic nonprogressive alignment algorithm that finds protein (or DNA) multiple sequence alignments with maximum expected accuracy.

Desktop app
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MAVID MAVID

MAVID

A multiple sequence alignment program suitable for the alignment of large…

A multiple sequence alignment program suitable for the alignment of large numbers of DNA sequences.

Desktop app
Opal Opal

Opal

A package for aligning multiple biological sequences. Opal attains accuracy on…

A package for aligning multiple biological sequences. Opal attains accuracy on par with the state-of-the-art without altering the alignment scoring function by increasing gap penalties near…

Desktop app
Pecan Pecan

Pecan

A Java consistency based multiple sequence alignment program.

A Java consistency based multiple sequence alignment program.

Desktop app
PSAlign PSAlign

PSAlign

A multiple sequence alignment program that finds a multiple alignment of k…

A multiple sequence alignment program that finds a multiple alignment of k sequences which preserves k-1 pairwise alignments as specified by edges of a given tree in polynomial time without using a…

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RevTrans RevTrans

RevTrans

Constructs a multiple DNA alignment by: (i) translating the DNA; (ii) aligning…

Constructs a multiple DNA alignment by: (i) translating the DNA; (ii) aligning the resulting peptide sequences; and (iii) building a multiple DNA alignment by 'reverse translation' of the…

Desktop app
StatAlign StatAlign

StatAlign

An Extendable Software Package for Joint Bayesian Estimation of Alignments and…

An Extendable Software Package for Joint Bayesian Estimation of Alignments and Evolutionary Trees.

Desktop app
Stemloc-AMA Stemloc-AMA

Stemloc-AMA

A novel approach to RNA multiple alignment which couples a generative…

A novel approach to RNA multiple alignment which couples a generative probabilistic model of sequence and structure with an efficient sequence annealing approach for exploring the space of multiple…

Desktop app
Base-By-Base Base-By-Base

Base-By-Base

A whole genome pairwise and multiple alignment editor. The program highlights…

A whole genome pairwise and multiple alignment editor. The program highlights differences between pairs of alignments and allows the user to easily navigate large alignments of similar sequences.…

Web app
Fast Statistical… Fast Statistical Alignment

FSA Fast Statistical Alignment

A program for the alignment of multiple biological sequences that is both…

A program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice.

Web app
Alignment-To-HTML Alignment-To-HTML

Alignment-To-HTML

First HTML-based interactive visualization for annotated multiple sequence…

First HTML-based interactive visualization for annotated multiple sequence alignments.

Desktop app
Cactus Cactus

Cactus

Uses a cactus graph (aka cactus tree), a graph in which any edge is a member of…

Uses a cactus graph (aka cactus tree), a graph in which any edge is a member of at most one simple cycle, to construct a genome alignment.

Desktop app
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Clustal W/Clustal X Clustal W/Clustal X

Clustal W/Clustal X

Multiple alignment of nucleic acid and protein sequences.

Multiple alignment of nucleic acid and protein sequences.

Desktop app
SeQuence alIgnmeNT Deprecated SeQuence alIgnmeNT

SQUINT SeQuence alIgnmeNT

Aligns sequence, combines both automated progressive sequence alignment with…

Aligns sequence, combines both automated progressive sequence alignment with facilities for manual editing. SQUINT imports nucleotide or amino acid sequence multiple alignment files in standard…

Desktop app
Infernal Infernal

Infernal

It is for searching DNA sequence databases for RNA structure and sequence…

It is for searching DNA sequence databases for RNA structure and sequence similarities.

Curators for Multiple sequence alignment

  • Laurent Mouchard's avatar image
    Laurent Mouchard
    University of Rouen, LITIS EA…
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