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Multiple sequence alignment software tools | Protein comparison analysis

Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task.Source text:(Pei and Grishin 2014)…
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…

MSAProbs-MPI
Desktop

MSAProbs-MPI

A state-of-the-art protein multiple sequence alignment tool based on hidden…

A state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. MSAProbs can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale…

PRALINE
Web

PRALINE Profile ALIgNmEnt

A toolkit for multiple sequence alignment. PRALINE provides various alignment…

A toolkit for multiple sequence alignment. PRALINE provides various alignment optimization strategies to address the different situations that call for protein multiple sequence alignment: global…

ProbCons
Web

ProbCons

A practical tool for progressive protein multiple sequence alignment based on…

A practical tool for progressive protein multiple sequence alignment based on probabilistic consistency. We evaluate its performance on several standard alignment benchmark data sets. On the…

Uniclust
Dataset

Uniclust

Analyses protein sequence, predicts function and searches sequence. Uniclust…

Analyses protein sequence, predicts function and searches sequence. Uniclust databases cluster UniProtKB sequences at the level of 90%, 50% and 30% pairwise sequence identity. The sequences in the…

PSI/TM-Coffee
Web
Desktop

PSI/TM-Coffee

Performs multiple sequence alignment (MSA) of proteins by combining homology…

Performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative…

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…

eShadow
Web

eShadow evolutionary phylogenetic SHADOWing of closely related species

Allows user to analyze any closely related sequences. eShadow studies multiple…

Allows user to analyze any closely related sequences. eShadow studies multiple protein alignments and identifies functional elements. It incorporates two distinct approaches for finding functional…

PVS
Web

PVS Protein Variability Server

Provides absolute sequence variability estimates ‘per site’ in a multiple…

Provides absolute sequence variability estimates ‘per site’ in a multiple protein-sequence alignment (MSA). PVS returns the selected reference sequence with the variable positions masked, as well…

KAPPA
Desktop

KAPPA Key Aminoacid Pattern-based Protein analyzer

Automatically searches sequence in the fields of discovery and clustering of…

Automatically searches sequence in the fields of discovery and clustering of ‘X-rich proteins’. KAPPA extracts and compares cysteine patterns by means of a quantitative similarity index called…

PROMALS
Web

PROMALS

Constructs multiple protein sequence alignments using information from database…

Constructs multiple protein sequence alignments using information from database searches and secondary structure prediction.

SABmark
Desktop

SABmark Sequence and structure Alignment Benchmark

Designed to assess the performance of both multiple and pairwise (protein)…

Designed to assess the performance of both multiple and pairwise (protein) sequence alignment algorithms, and is extremely easy to use.

Probalign
Desktop

Probalign

Uses partition function posterior probability estimates to compute maximum…

Uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments.

SMS
Web

SMS STING Millennium Suite

Provides a variety of algorithms and validated data, wrapped-up in a user…

Provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing…

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…

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…

COMPASS
Web
PRALINETM
Web

PRALINETM

Aligns undivided sequences instead and applies substitution scores from the…

Aligns undivided sequences instead and applies substitution scores from the PHAT matrix only where predictions are 100% consistent. PRALINETM is a multiple sequence alignment program with many…

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.

PROMALS3D
Web

PROMALS3D

Constructs alignments for multiple protein sequences and/or structures using…

Constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and…

ProDA
Desktop

ProDA Protein Domain Aligner

Provides a useful method for automated multiple alignment of multi-domain…

Provides a useful method for automated multiple alignment of multi-domain proteins. ProDA is an integrated alignment methodology designed to (i) computes local alignments for every pair of sequences,…

MP-T
Web

MP-T Membrane Protein Threader

Performs sequence to structure alignment for the homology modelling of membrane…

Performs sequence to structure alignment for the homology modelling of membrane proteins. The Membrane Protein Threader is a progressive multiple alignment method specifically use on membrane protein…

MIToS.jl
Desktop
ContTest
Dataset

ContTest

A benchmark for protein multiple sequence alignments containing many thousands…

A benchmark for protein multiple sequence alignments containing many thousands of sequences in each test case, and which is based on empirical biological data. We rank popular multiple sequence…

KMAD
Desktop
Web
DECIPHER
Desktop

DECIPHER

A context-aware program for sequence alignment. DECIPHER exhibited excellent…

A context-aware program for sequence alignment. DECIPHER exhibited excellent performance in the range of hundreds to thousands of sequences, with little decrease from maximal accuracy.

GlycoSiteAlign
Web

GlycoSiteAlign

Aligns amino acid sequences of variable length surrounding glycosylation sites…

Aligns amino acid sequences of variable length surrounding glycosylation sites depending on the knowledge of glycan structure. GlycoSiteAlign is an exploratory resource intended for the…

FAMSA
Desktop

FAMSA Fast and Accurate Multiple Sequence Aligner

Allows to make accurate and fast alignment of thousands of protein sequences.…

Allows to make accurate and fast alignment of thousands of protein sequences. FAMSA is made as a fast algorithm working on multiple sequence alignment designed for huge protein families. It requires…

MAPGAPS
Desktop

MAPGAPS Multiply-Aligned Profiles for Global Alignment of Protein Sequences

Uses a multiple-profile alignment to ‘map the gaps’ (i.e. the insertions…

Uses a multiple-profile alignment to ‘map the gaps’ (i.e. the insertions and deletions, both large and small) between distantly related proteins. The multiple-profile alignment serves both as a…

PsychoProt
Web
Desktop

PsychoProt Physical CHemistry Of Protein variability

A web app and a package to study about protein modeling, evolution and design.…

A web app and a package to study about protein modeling, evolution and design. PsychoProt helps to (i) unveil protein structure-function relationships from experiments and from alignments that are…

PRRN
Web
Desktop

PRRN

Allows multiple sequence alignment. PRRN is an iterative multiple protein…

Allows multiple sequence alignment. PRRN is an iterative multiple protein sequence alignment (MPSA) method.

ALN
Web
Desktop

ALN

Allows alignment of a pair of nucleotide, amino acid sequences or groups of…

Allows alignment of a pair of nucleotide, amino acid sequences or groups of sequences. ALN is a spliced alignment program that can use a generalized profile as template.

INVHOGEN
Dataset

INVHOGEN INVertebrate HOmologous GENes

Provides invertebrate protein sequences from UniProt organized into families of…

Provides invertebrate protein sequences from UniProt organized into families of homologous genes defined by sequence similarity. INVHOGEN offers a multiple protein alignment, a maximum likelihood…

Dialign-Pfam
Web

Dialign-Pfam

Identifies possible domains in protein sequences by scanning the input…

Identifies possible domains in protein sequences by scanning the input sequences using HMMER against PFAM database. Dialign-Pfam then uses this information to align protein sequences using Dialign.

aSVARAP
Desktop

aSVARAP amino acid Sequence VARiability Analysis Program

Analyses the variability along multiple amino acid sequences alignments.…

Analyses the variability along multiple amino acid sequences alignments. aSVARAP is derived from SVARAP (Sequence VARiability Analysis Program) and is dedicated to amino acid sequences. It combine…

Exonerate
Desktop

Exonerate

A generic tool for pairwise sequence comparison. Exonerate allows you to align…

A generic tool for pairwise sequence comparison. Exonerate allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics. The Exonerate…

MSAIndelFR
Desktop

MSAIndelFR

An efficient algorithm for multiple protein sequence alignment incorporating a…

An efficient algorithm for multiple protein sequence alignment incorporating a new variable gap penalty function. The algorithm incorporates the information on the predicted locations of IndelFRs and…

Facet
Desktop

Facet feature-based accuracy estimator

Outperforms the best prior approaches to assessing alignment quality. Facet is…

Outperforms the best prior approaches to assessing alignment quality. Facet is a package that computes a single estimate of accuracy as a linear combination of efficiently-computable feature…

MMSA
Desktop

MMSA Modular Multiple Sequence Aligner

Allows users to perform multiple protein sequence alignments. MMSA is developed…

Allows users to perform multiple protein sequence alignments. MMSA is developed to provide a modular structure, using a SeqAn sequence alignment library, where different components can be…

BaCoCa
Desktop

BaCoCa BAse COmposition CAlculator

Identifies biases in aligned sequence data which potentially mislead…

Identifies biases in aligned sequence data which potentially mislead phylogenetic reconstructions. BaCoCa allows a parallel determination of a suite of different statistical properties of alignments…

GaussDCA
Desktop

GaussDCA Gaussian Direct Coupling Analysis

A multivariate Gaussian modeling approach as a variant of direct-coupling…

A multivariate Gaussian modeling approach as a variant of direct-coupling analysis. With GaussDCA, the discrete amino-acid variables are replaced by continuous Gaussian random variables. The…

QuickProbs
Desktop

QuickProbs

A fast multiple sequence alignment algorithm. QuickProbs is a variant of…

A fast multiple sequence alignment algorithm. QuickProbs is a variant of MSAProbs customised for graphics processors. QuickProbs uses new, graphics processor specific, intra-task parallel algorithms…

Seqmol
Desktop

Seqmol Sequences and molecules

Identifies stable or weak complexes by calculating Kd for formation of…

Identifies stable or weak complexes by calculating Kd for formation of interfaces. SEQMOL is a protein data bank (PDB) structure analysis suite. It can be used to align multiple protein and DNA…

PicXAA
Desktop
Web

PicXAA ProbabilistIC maXimum Accuracy Alignment

Finds the multiple sequence alignment (MSA) with the maximum expected accuracy…

Finds the multiple sequence alignment (MSA) with the maximum expected accuracy (MEA). PicXAA is a probabilistic non-progressive alignment algorithm which takes a greedy approach to probabilistically…

COBALT
Desktop
Web

COBALT

A constraint based alignment tool that implements a general framework for…

A constraint based alignment tool that implements a general framework for multiple alignment of protein sequences. COBALT finds a collection of pairwise constraints derived from database searches,…

SATCHMO
Desktop

SATCHMO Simultaneous Alignment and Tree Construction using Hidden Markov mOdels

Constructs simultaneously a tree and a set of multiple sequence alignments, one…

Constructs simultaneously a tree and a set of multiple sequence alignments, one for each internal node of the tree. SATCHMO generates profile hidden Markov models (HMM) at each node; these are used…

SPEM
Desktop
Web

SPEM

Aligns multiple sequences using pre-processed sequence profiles and predicted…

Aligns multiple sequences using pre-processed sequence profiles and predicted secondary structures for pairwise alignment, consistency-based scoring for refinement of the pairwise alignment and a…

LogoBar
Desktop

LogoBar

A Java application to display protein sequence logos. With this application you…

A Java application to display protein sequence logos. With this application you can generate protein sequence logos from multiple sequence alignments on your own computer, and you will get an…

PROCAIN
Web

PROCAIN

A method for the comparison of two multiple alignments of protein sequences.

A method for the comparison of two multiple alignments of protein sequences.

CUBE
Web

CUBE comparative analysis of protein sequences

Offers access to two scoring programs, one focusing on the conservation within…

Offers access to two scoring programs, one focusing on the conservation within a set of sequences, and the other on the specialization across several families. Cube is structured to highlight the…

LoCo
Desktop

LoCo Local Covariation

An alignment curation tool that integrates local covariation scores with the…

An alignment curation tool that integrates local covariation scores with the Jalview alignment editor. LoCo shows how local covariation is capable of identifying alignment errors due to the reduction…

ProfileGrids
Desktop

ProfileGrids

A Java-based multiple sequence alignment tool that generates ProfileGrids for…

A Java-based multiple sequence alignment tool that generates ProfileGrids for analysis and export. It provides both command-line support and a graphical user interface.

Sequence…
Desktop

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.

MSACompro
Desktop

MSACompro

A method to incorporate predicted secondary structure, relative solvent…

A method to incorporate predicted secondary structure, relative solvent accessibility, and residue-residue contact information into the most accurate posterior probability-based MSA methods to…

BsFinder
Desktop

BsFinder

Identifies regions of binding sites on the proteins. BsFinder first proceeds to…

Identifies regions of binding sites on the proteins. BsFinder first proceeds to a local sequence alignment then detects protein surface, and finally compares 3d structures. The software can perform…

SuiteMSA
Desktop

SuiteMSA Suite of Multiple Sequence Alignment

Provides researchers easy access to a sequence evolution simulator, reference…

Provides researchers easy access to a sequence evolution simulator, reference alignments generated by the simulator, and a series of tools to evaluate the performance of the multiple sequence…

webPRANK
Desktop
Web

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…

MergeAlign
Web

MergeAlign

Constructs a consensus multiple sequence alignment from multiple independent…

Constructs a consensus multiple sequence alignment from multiple independent alignments. Using dynamic programming MergeAlign efficiently combines individual multiple sequence alignments to generate…

BlockLogo
Web

BlockLogo

A web-server application for the visualization of protein and nucleotide…

A web-server application for the visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from…

H2PDB
Web

H2PDB

Maps the amino acid variability within a protein sequence alignment onto a 3D…

Maps the amino acid variability within a protein sequence alignment onto a 3D structure. H2PDB employs the Shannon Entropy equation (H). It returns the sequence variability in the form of a B-factor.

BoxShade
Web
Desktop

BoxShade

Allows printouts of multiple aligned protein or DNA sequences. BoxShade offers…

Allows printouts of multiple aligned protein or DNA sequences. BoxShade offers various output formats

amap-align
Desktop

amap-align

Allows to align multiple sequences. amap-align is based on a sequence annealing…

Allows to align multiple sequences. amap-align is based on a sequence annealing approach.

edialign
Desktop

edialign

Constructs alignments from gapfree pairs of similar segments of the sequences.…

Constructs alignments from gapfree pairs of similar segments of the sequences. edialign is an EMBOSS version of the program DIALIGN2. If (possibly) coding nucleic acid sequences are to be aligned,…

NAP
Desktop

NAP Nucleotide Amino Acid Alignment

Uses to annotate coding region features in a genomic sequence automatically…

Uses to annotate coding region features in a genomic sequence automatically because it has several special features that were designed accurately to align a genomic DNA sequence to a related protein…

PSAweb
Web

PSAweb

A web server, developed to analyze the amino acid sequence and multiple…

A web server, developed to analyze the amino acid sequence and multiple sequence alignment of proteins. This is a comprehensive on-line Internet tool that allows the rapid visualization of an…

GLProbs
Desktop

GLProbs

A simple and effective approach to improve the accuracy of multiple sequence…

A simple and effective approach to improve the accuracy of multiple sequence alignment.

ABA
Desktop

ABA A-Bruijn Aligner

Offers a representation for a multiple alignment from the A-Bruijn graph. ABA…

Offers a representation for a multiple alignment from the A-Bruijn graph. ABA produces multiple alignments of sequences including shuffled and repeated regions. ABA is also applicable to the…

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