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Multiple nucleotide sequence alignment software tools | Comparative genomics

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…
MAFFT
Web
Desktop

MAFFT

Allows alignment of multiple sequences. MAFFT provides a range of different…

Allows alignment of multiple sequences. MAFFT provides a range of different methods such as L-INS-I or FFT-NS-2. It permits to add unaligned sequences into an existing alignment. This tool can…

HAlign
Desktop
Web

HAlign

Provides a fast-multiple similar DNA/RNA sequence alignment method. HAlign is a…

Provides a fast-multiple similar DNA/RNA sequence alignment method. HAlign is a multiple sequence alignment (MSA) application based on the centre star strategy. The goal of this application is…

T-Coffee
Desktop
Web

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…

Clustal Omega
Desktop
Web

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…

PREFAB
Dataset

PREFAB Protein Reference Alignment Benchmark

Tests multiple sequence alignment methods. PREFAB is a test set which exploits…

Tests multiple sequence alignment methods. PREFAB is a test set which exploits methodology, test data and statistical methods that have previously been applied to alignment accuracy assessment. It…

Pecan
Desktop

Pecan

Disregards genomic location information and treats the segments simply as…

Disregards genomic location information and treats the segments simply as sequences. Pecan is a colinear alignment method that makes posterior decoding and the consistency methodology practical for…

LocARNA
Web
Desktop

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.…

BAli-Phy
Desktop

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…

DIALIGN
Web

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…

MUSCLE
Web

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…

Clustal…
Desktop
Web

Clustal W/Clustal X

Multiple alignment of nucleic acid and protein sequences.

Multiple alignment of nucleic acid and protein sequences.

ProAlign
Desktop

ProAlign

Allows to study alignment of sequences. ProAlign contains a graphical interface…

Allows to study alignment of sequences. ProAlign contains a graphical interface permitting to: (1) separate the unreliable alignment regions; (2) export alignments to other software; (3) observe the…

PAL2NAL
Web
Desktop

PAL2NAL

Converts a protein sequence alignment into the corresponding codon alignment.…

Converts a protein sequence alignment into the corresponding codon alignment. PAL2NAL is a web server allowing users to obtain codon alignments for specific regions of interest, such as functional…

BAliBASE
Dataset

BAliBASE

Provides high quality reference alignments based on 3D structural…

Provides high quality reference alignments based on 3D structural superpositions. BAliBASE is a large scale benchmarks specifically designed for multiple sequence alignment. The alignment test cases…

Mulan
Web

Mulan

Allows user to study phenotypic differences in vertebrate species. Mulan is a…

Allows user to study phenotypic differences in vertebrate species. Mulan is a comparative tool that generates multiple-sequence local alignments (MSLAs). It contains an alignment engine consisting of…

TranslatorX
Web
Desktop

TranslatorX

Provides an approach to clean nucleotide alignments based on initial GBlocks…

Provides an approach to clean nucleotide alignments based on initial GBlocks cleaning of the corresponding amino acid alignment. TranslatorX is a web application that generates back-translated…

RevTrans
Desktop
Web

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…

UPP
Desktop

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…

Cactus
Desktop

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.

StatAlign
Desktop

StatAlign

Samples from the joint posterior distribution of phylogenies, alignments and…

Samples from the joint posterior distribution of phylogenies, alignments and evolutionary parameters by applying the Markov chain Monte Carlo (MCMC) method. StatAlign also offers tools for efficient…

Mugsy
Desktop

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…

Base-By-Base
Desktop

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.…

FSA
Web

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.

NAST-iEr
Desktop

NAST-iEr

Aligns a single raw nucleotide sequence against one or more NAST formatted…

Aligns a single raw nucleotide sequence against one or more NAST formatted sequences. NAST-iEr is an alignment algorithm involves global dynamic programming profile alignment to fixed…

GramDist
Desktop

GramDist

Allows users to work about clustering large data sets of 16S rDNA sequences…

Allows users to work about clustering large data sets of 16S rDNA sequences based on the inherent grammar of DNA and RNA sequences. GramDist utilizes a grammar-based distance metric to identify…

Opal
Desktop

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…

PASTASpark
Desktop

PASTASpark Practical Alignments using SATé and TrAnsitivity

Allows to improve the performance of the alignment phase of practical…

Allows to improve the performance of the alignment phase of practical alignments using saté and transitivity (PASTA). PASTASpark allows to execute PASTA on a distributed memory cluster making use of…

Phylo-Node
Desktop

Phylo-Node

Provides sequence retrieval, primer design, alignment, phylogeny reconstruction…

Provides sequence retrieval, primer design, alignment, phylogeny reconstruction from a single toolkit. phylo-node is a Node.js toolkit that offers simple customization and portability options through…

M2Align
Desktop

M2Align Multi-objective Multiple Sequence Alignment

Permits to solve multiple sequence alignment (MSA) problems by using…

Permits to solve multiple sequence alignment (MSA) problems by using multi-objective metaheuristics. M2Align is a method based on the jMetal multi-objective framework, which is extended with an…

Historian
Desktop

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…

msa
Desktop

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,…

Alignment-To-HT…
Web

Alignment-To-HTML

First HTML-based interactive visualization for annotated multiple sequence…

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

Stemloc-AMA
Desktop

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…

eProbalign
Desktop
Web

eProbalign

Computes maximal expected accuracy multiple sequence alignments from partition…

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

Pro-Coffee
Web

Pro-Coffee

Aligns homologous promoter regions. Pro-Coffee uses a dinucleotide substitution…

Aligns homologous promoter regions. Pro-Coffee uses a dinucleotide substitution matrix estimated on alignments of functional binding sites from TRANSFAC. Its better performance goes along with a more…

VCFtoTree
Desktop

VCFtoTree

Extracts variants from haplotypes and generates aligned complete sequences for…

Extracts variants from haplotypes and generates aligned complete sequences for the region of interest. VCFtoTree allows integration of sequences from reference genomes of Chimpanzee, and Rhesus…

NucAmino
Desktop

NucAmino

Aligns a virus nucleotide sequence to a reference amino acid sequence. NucAmino…

Aligns a virus nucleotide sequence to a reference amino acid sequence. NucAmino is a program with several advantages compared with existing programs for clinical laboratories performing Human…

NucDiff
Desktop

NucDiff

Aligns sequences and outputs information about aligned sequence regions.…

Aligns sequences and outputs information about aligned sequence regions. NucDiff is a computational package that uses the NUCmer, delta-filter and show-snps programs from MUMmer for sequence…

CMSA
Desktop

CMSA CPU Multiple Sequences Alignment

Represents a multiple sequence alignment (MSA) system for large-scale datasets…

Represents a multiple sequence alignment (MSA) system for large-scale datasets on the heterogeneous CPU/GPU platform. CMSA focuses on the alignment of similar RNA/DNA sequences. It can perform and…

HomBlocks
Desktop

HomBlocks

Constructs multi-gene alignments in a time-consuming way when compared with the…

Constructs multi-gene alignments in a time-consuming way when compared with the conventional method. HomBlocks can automatically recognize locally collinear blocks among organelle genomes and…

TFcompare
Web

TFcompare

Superposes pairs of transcription factor (TF)-DNA complexes in order to obtain…

Superposes pairs of transcription factor (TF)-DNA complexes in order to obtain structural alignments of cis elements recognized by homologous TFs. TFcompare calculates structural alignments between…

Séance
Desktop

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…

FLEA
Web
Desktop

FLEA Full-Length Envelope Analyzer

Analyzes longitudinal full-length sequences. FLEA is a pipeline for handling…

Analyzes longitudinal full-length sequences. FLEA is a pipeline for handling long read HIV-1 env sequencing data from within host viral populations. It can be accessed through a web browser or on a…

RIFRAF
Desktop

RIFRAF Reference-Informed Frame-Resolving multiple Alignment Free consensus algorithm

Allows users to realize accurate predictions. RIFRAF is an algorithm that can…

Allows users to realize accurate predictions. RIFRAF is an algorithm that can detect true frameshift-causing indels and keep them while removing spurious indels. It considers evidence from both the…

RautiainenEtAl2…
Algorithm

RautiainenEtAl2017

Allows users to study the problem of semi-global sequence-to-graph alignment.…

Allows users to study the problem of semi-global sequence-to-graph alignment. This algorithm permits threating a query sequence and a reference sequence. It assists users in finding an optimal…

MASC
Desktop

MASC Multiple sequence Alignment based on a Suffix tree and Center-star strategy

Allows users to perform multiple sequences alignments (MSA) among highly…

Allows users to perform multiple sequences alignments (MSA) among highly similar sequences. MASC is a standalone software which can be applied for MSA in linear time and for very high-throughput…

MoDMaps3D
Web

MoDMaps3D Molecular Distance Maps 3D

Computes and displays sequence and species relatedness. MoDMaps3D is an…

Computes and displays sequence and species relatedness. MoDMaps3D is an alignment-free web-tool using approximated information distance (AID) to quantify the pairwise differences in oligomer…

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RNA workbench
Server

RNA workbench

Establishes a central, redistributable workbench for scientists and programmers…

Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in…

Adaptive-Banded…
Desktop

Adaptive-Banded algorithm

Calculates pairwise semi-global alignment of nucleotide sequences.…

Calculates pairwise semi-global alignment of nucleotide sequences. Adaptive-Banded algorithm allows user to insert and delete rate while maintaining the band width to some small constant. This tool…

SPARSE
Desktop

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…

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