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This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment
List of sequence alignment software
List_of_sequence_alignment_software
subsection of the list of sequence alignment software. Multiple alignment visualization tools typically serve four purposes: Aid general understanding of large-scale
List of alignment visualization software
List_of_alignment_visualization_software
software List of alignment visualization software Alignment-free sequence analysis De novo sequence assemblers List of gene prediction software List of
Lists of bioinformatics software
Lists_of_bioinformatics_software
Process in bioinformatics that identifies equivalent sites within molecular sequences
a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional
Sequence_alignment
software for molecular mechanics modeling Earth BioGenome Project List of sequence alignment software List of open-source healthcare software List of
List of open-source bioinformatics software
List_of_open-source_bioinformatics_software
Lists of software used in various branches of engineering
simulation software List of sequence alignment software List of software for nanostructures modeling List of software for nuclear engineering List of structural
Lists_of_engineering_software
Identification and study of genomic sequences
analysis Sequence mining Alignment-free sequence analysis List of sequence alignment software List of alignment visualization software List of phylogenetics
Sequence_analysis
Aligning molecular sequences using sequence and structural information
in Proteopedia.Org. Multiple sequence alignment List of sequence alignment software Structural Classification of Proteins SuperPose Protein superfamily
Structural_alignment
This list of structural comparison and alignment software is a compilation of software tools and web portals used in pairwise or multiple structural comparison
Structural_alignment_software
software List of sequence alignment software List of gene prediction software List of RNA structure prediction software Comparison of software for molecular
Comparison of nucleic acid simulation software
Comparison_of_nucleic_acid_simulation_software
homeostasis List of sequence alignment software List of open-source healthcare software List of open-source bioinformatics software List of proprietary
List of biomedical cybernetics software
List_of_biomedical_cybernetics_software
sequence alignment software List of open-source bioinformatics software List of open-source health software List of biomedical cybernetics software List of freeware
List of proprietary bioinformatics software
List_of_proprietary_bioinformatics_software
for Alignment Evaluation) is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to guide
T-Coffee
Conformance of AI to intended objectives
In the field of artificial intelligence (AI), alignment aims to steer AI systems toward a person's or group's intended goals, preferences, or ethical principles
AI_alignment
Method of DNA sequence reconstruction
De novo sequence assemblers. For a list of mapping aligners, see List of sequence alignment software § Short-read sequence alignment. Some of the common
Sequence_assembly
List of sequence alignment software. Short aligners are able to align continuous reads (not containing gaps result of splicing) to a genome of reference
List of RNA-Seq bioinformatics tools
List_of_RNA-Seq_bioinformatics_tools
Software project for the analysis of genomic data
software portal Biology portal Computational biology Bioinformatics List of open source bioinformatics software List of sequence alignment software R
Bioconductor
Branch of bioinformatics
of sequences, genomes, alignments, phylogenies, macromolecular structures, systems biology, microscopy, and magnetic resonance imaging data. Software
Biological_data_visualization
Computational biologist
prediction. His group has developed widely cited software tools and techniques: Alscript (multiple sequence alignment formatting), Jalview (data integration and
Geoff_Barton_(scientist)
File format for DNA or protein sequences
codes. The format allows for sequence names and comments to precede the sequences. It originated from the FASTA software package and has since become
FASTA_format
Compilation of software used to produce phylogenetic trees
2014). "AliGROOVE--visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support". BMC
List of phylogenetics software
List_of_phylogenetics_software
Bioinformatics software
faster software solutions. The first major version of DIAMOND was published in November 2014 and focused on alignment sensitivity at above 50% sequence identity
DIAMOND_(biotechnology)
File format for genomic features
also available. Distributed Annotation System Variant Call Format Sequence alignment "GFF/GTF File Format". Ensembl. Archived from the original on 2022-06-15
General_feature_format
Algorithm for determining similar regions between two molecular sequences
local sequence alignment; that is, for determining similar regions between two strings of nucleic acid sequences or protein sequences. Instead of looking
Smith–Waterman_algorithm
Software package for sequence analysis
commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or nucleotide sequences, and to
HMMER
and the addition of new sequences to existing alignments. There have been many variations of the MAFFT software, some of which are listed below: MAFFT –
MAFFT
Bioinformatics search algorithm
local alignment search tool) is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins
BLAST_(biotechnology)
Suite of free genome analysis software by Nvidia
pipeline inside their workflows. List of bioinformatics software List of sequence alignment software "Clara for Genomics". NVIDIA. Retrieved 8 July 2024.
Nvidia_Parabricks
This is a list of aerospace engineering software which is used for computational fluid dynamics, finite element method structural analysis, flight dynamics
List of aerospace engineering software
List_of_aerospace_engineering_software
Similar DNA, RNA or protein sequences within genomes or among species
developmental biology NAPP (database) Segregating site Sequence alignment Sequence alignment software UCbase "Clustal FAQ #Symbols". Clustal. Archived from
Conserved_sequence
Expressed sequence tag Gene expression Homology List of phylogenetics software Phylogenetics Phylogenetic tree RNA RNA-Seq Sequence alignment Synonymous
Phylogenetic inference using transcriptomic data
Phylogenetic_inference_using_transcriptomic_data
homologs detectable by sequence alignment. The two methods both predict protein structure from a template. Given a protein sequence, protein threading first
RAPTOR_(software)
list of civil engineering software used in the design, analysis, modeling, construction, and management of civil engineering projects. The software includes
List of civil engineering software
List_of_civil_engineering_software
Computer software for bioinformatics
computer software for bioinformatics. It helps biologists to analyze various biological genetics data, such as sequences, annotations, multiple alignments, phylogenetic
UGENE
This list of RNA structure prediction software is a compilation of software tools and web portals used for nucleic acid structure prediction. The single
List of RNA structure prediction software
List_of_RNA_structure_prediction_software
Software for statistical analysis of molecular evolution
application. Multiple sequence alignment One of the challenges associated with evolutionary genetic analysis is the presence of ambiguous states such
Molecular Evolutionary Genetics Analysis
Molecular_Evolutionary_Genetics_Analysis
This list of phylogenetic tree viewing software is a compilation of software tools and web portals used in visualizing phylogenetic trees. 1 "All" refers
List of phylogenetic tree visualization software
List_of_phylogenetic_tree_visualization_software
This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling
List of protein structure prediction software
List_of_protein_structure_prediction_software
spectrometry data format: for a list of mass spectrometry data viewers and format converters. List of protein structure prediction software Cox, Jürgen; Neuhauser
List of mass spectrometry software
List_of_mass_spectrometry_software
open-source software package for sensitive protein sequence searching. It contains programs that can search for similar protein sequences in protein sequence databases
HH-suite
Molecular modelling software
visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories
UCSF_Chimera
Algorithm used in data compression
known, nearly complete sequence of the organism in question (which may be up to several billion base pairs long). A number of alignment programs, specialized
Burrows–Wheeler_transform
Pairwise sequence alignment algorithm
BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC)
BLAT_(bioinformatics)
File format for sequence alignments
Reference-oriented Alignment Map (CRAM) is a compressed columnar file format for storing biological sequences aligned to a reference sequence, initially devised
CRAM_(file_format)
This is a list of mechanical engineering software used for the engineering design, analysis, simulation, and manufacturing of mechanical systems and components
List of mechanical engineering software
List_of_mechanical_engineering_software
Collection of open-source Python software tools for computational biology
in scripts or incorporated into their software. Biopython contains a standard sequence class, sequence alignment, and motif analysis tools. It also has
Biopython
Software engineering approach to designing and developing information systems
Data engineering is a software engineering approach to the building of data systems, to enable the collection and usage of data. This data is usually used
Data_engineering
Study of making products from raw materials
simulation software such as ASPEN, Super-Pro to find out the break even point, net present value, marginal sales, marginal cost, return on investment of the
Process_engineering
a list of software tools and web portals used for gene prediction. Gene prediction List of RNA structure prediction software Comparison of software for
List of gene prediction software
List_of_gene_prediction_software
Topics referred to by the same term
cereal, rice, and milk diet CRAM (file format), a compressed genome sequence alignment file Cognitive robotic abstract machine, a cognitive architecture
Cram
Lab technique in cellular biology
of genome guided alignment (mapping) tools can be further used by tools such as Cufflinks or StringTie to reconstruct contiguous transcript sequences
RNA-Seq
find global alignment between two sequences Smith–Waterman algorithm: find local sequence alignment Exchange sorts Bubble sort: for each pair of indices,
List_of_algorithms
enhanced version of the Vector Alignment Search Tool (VAST). List of molecular graphics systems Molecular graphics List of software for molecular mechanics
Cn3D
List of software used in plasma physics and magnetohydrodynamics simulations
software List of computational fluid dynamics software List of computational chemistry software List of computational materials science software List
List of plasma physics software
List_of_plasma_physics_software
Engineering discipline focused on robots
software and AI. Robotics engineering combines several technical disciplines, all of which contribute to the performance, autonomy, and robustness of
Robotics_engineering
Epidemiology method
from the data (including the sequence alignment), then the analysis becomes a hierarchical model in which the problem of phylogenetic reconstruction is
Source_attribution
File format for block-based Gzip compression
as part of SAM/BAM specification and SAMtools. It is a core component of the common BAM format (the binary version of the Sequence Alignment Map format)
BGZF
Topics referred to by the same term
a candidate phylum of bacteria Sustained Acoustic Medicine, a medical treatment for arthritis SAMtools (for Sequence Alignment Map), a data storage
Sam
Sub-sequence DNA in genetics
In genetics, an expressed sequence tag (EST) is a short sub-sequence of a cDNA sequence. ESTs may be used to identify gene transcripts, and were instrumental
Expressed_sequence_tag
Engineering approach to software development
maintainable software. The origins of the term software engineering have been attributed to various sources. The term appeared in a list of services offered
Software_engineering
Model of changes in a sequence over evolutionary time
in the case of proteins). Substitution models are used to calculate the likelihood of phylogenetic trees using multiple sequence alignment data. Thus,
Substitution_model
Field of algorithmic training
free and Copycenter alternative to MATLAB. There are a number of free and open-source software (FOSS) tools that support computational engineering. OpenSCAD
Computational_engineering
A sequence profiling tool in bioinformatics is a type of software that presents information related to a genetic sequence, gene name, or keyword input
Sequence_profiling_tool
Type of biological prediction
(April 2006). "A comparative study of available software for high-accuracy homology modeling: from sequence alignments to structural models". Protein Science
Protein_structure_prediction
Engineering discipline
(Datamine is a provider of the technology and the services required to plan and manage mining operations seamlessly.) Mining Software Mineral Exploration
Mining_engineering
Computational physics Computer simulation List of computational physics software List of plasma physics software List of software for nanostructures modeling IAEA
List of software for nuclear engineering
List_of_software_for_nuclear_engineering
Type of machine learning model
multiple sequence alignments (MSA) as input. ESMFold, Meta Platforms' embedding-based method for protein structure prediction, runs an order of magnitude
Large_language_model
Sub-discipline of electrical engineering
engineers may also work on a system's software. However, the design of complex software systems is often the domain of software engineering which falls under
Electronics_engineering
Academic discipline and occupational field
transportation engineering Highway engineering List of BIM software List of civil engineering software Pavement engineering Traffic engineering "Course
Transportation_engineering
Bioinformatician
of disease. As of October 2025, Li's papers on SAMtools and BWA (sequence alignment using the Burrows–Wheeler transform) have both been cited over 50
Heng_Li
graph theoretic sequence clustering algorithm JESAM: Open source parallel scalable DNA alignment engine with optional clustering software component UICluster:
Sequence_clustering
Method of protein structure prediction using other known proteins
structure of the query sequence, and on the production of a sequence alignment that maps residues in the query sequence to residues in the template sequence. It
Homology_modeling
Branch of engineering
using CAD software are also commonly used in finite element analysis (FEA) and computational fluid dynamics (CFD). Machine tools employ some sort of tool that
Manufacturing_engineering
Deep learning facial recognition system
consists of four modules: 2D alignment, 3D alignment, frontalization, and neural network. An image of a face is passed through them in sequence, resulting
DeepFace
Package) is a suite of bioinformatics software tools from the BGI Bioinformatics department enabling the assembly, alignment, and analysis of next generation
Short Oligonucleotide Analysis Package
Short_Oligonucleotide_Analysis_Package
Software for the visualisation of macromolecules
a multiple sequence alignment program, the responsible Java class can be freely used in other applications. Free and open-source software portal Science
RasMol
Computational methods exploit the sequence signatures of disorder to predict whether a protein is disordered, given its amino acid sequence. The table below, which
List of disorder prediction software
List_of_disorder_prediction_software
Artificial intelligence field of study
consequences arising from artificial intelligence systems. It encompasses AI alignment (which aims to ensure AI systems behave as intended), monitoring AI systems
AI_safety
Engineering discipline specializing in the design of computer hardware
or CompE) is a branch of engineering specialized in developing computer hardware and software. It integrates several fields of electrical engineering
Computer_engineering
Branch of engineering which deals with the optimization of complex processes or systems
non-exhaustive list. While some industrial engineers focus exclusively on one of these sub-disciplines, many deal with a combination of sub-disciplines
Industrial_engineering
Branch of engineering regarding drugs
Pharmaceutical engineering is a branch of engineering focused on discovering, formulating, and manufacturing medication, analytical and quality control
Pharmaceutical_engineering
Engineering discipline that deals with control systems
the process variable output of the plant to the same value as the setpoint. For sequential and combinational logic, software logic, such as in a programmable
Control_engineering
Monthly scientific journal established 1994
Journal of Computational Biology. Mary Ann Liebert. Retrieved 4 November 2025. "Journal of Computational Biology". Web of Science Master Journal List. Clarivate
Journal of Computational Biology
Journal_of_Computational_Biology
Software in bioinformatics
De novo sequence assemblers are a type of program that assembles short nucleotide sequences into longer ones without the use of a reference genome. These
De_novo_sequence_assemblers
Use of software for engineering design and analysis
better alignment between 3D CAE, 1D system simulation, and physical testing. This should increase modeling realism and calculation speed. CAE software companies
Computer-aided_engineering
also References List of filename extensions List of file formats "F4V/FLV Technology Center". Adobe. Retrieved 2020-09-15. "Alignment Fileformats". 22
List of filename extensions (F–L)
List_of_filename_extensions_(F–L)
Engineering discipline focused on the design and operation of chemical plants
principles were used to produce DNA sequences in large quantities. Chemical engineering design concerns the creation of plans, specifications, and economic
Chemical_engineering
File format for sequences and quality scores
Sequencing Analysis Software User Guide: For Pipeline Version 1.5 and CASAVA Version 1.0, dated August 2009 PDF[dead link] Sequence/Alignment Map format Version
FASTQ_format
Method used to investigate protein structure
helixes and coils) from the primary sequence. PSIPRED is available as a web service and as software. The software is distributed as source code, licensed
PSIPRED
German researcher and professor of bioinformatics
under the supervision of Kurt Mehlhorn and Hans-Peter Lenhof. His doctoral thesis, titled "A Polyhedral Approach to Sequence Alignment Problems", focused
Knut_Reinert
Study of RNA transcripts
can circumvent the need for an exact alignment of a read to a reference sequence altogether. The kallisto software method combines pseudoalignment and
Transcriptomics_technologies
Machine learning software library in C++
Free and open-source software portal Shogun is a free, open-source machine learning software library written in C++. It offers numerous algorithms and
Shogun_(toolbox)
Andreas; Holm, Liisa (2000). "Rapid automatic detection and alignment of repeats in protein sequences". Proteins: Structure, Function, and Genetics. 41 (2):
List of protein tandem repeat annotation software
List_of_protein_tandem_repeat_annotation_software
Matrix representing the frequency of evolution of a protein or nucleotide sequence
context of amino acid or DNA sequence alignments, where they are used to calculate similarity scores between the aligned sequences. In the process of evolution
Substitution_matrix
modeling tool used in the software development industry. The term Misuse Case or mis-use case is derived from and is the inverse of use case. The term was
Misuse_case
File format for sequence data
summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of SNP/indel calling and alignment. It was first used
Pileup_format
Combination of electronics and mechanics
since they have strong mechanical and electronical background. Knowledge of software applications such as computer-aided design and computer-aided manufacturing
Mechatronics
similar sequence of known structure), before aligning the query and template sequences. EsyPred3D then build the 3D models using the alignment and the
ESyPred3D
resource based on 5090 organisms and 2502 viruses. It provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation
List_of_biological_databases
Software for protein modeling and analysis
of results. RaptorX Server currently generates the following results: 3-state and 8-state secondary structure prediction, sequence-template alignment
RaptorX
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LIST OF-SEQUENCE-ALIGNMENT-SOFTWARE
LIST OF-SEQUENCE-ALIGNMENT-SOFTWARE
Boy/Male
Indian, Sanskrit
Order; Sequence
Female
English
 Variant spelling of English Liza, LISA means "God is my oath." Compare with another form of Lisa.
Female
French
French form of German Elise, ÉLISE means "God is my oath."Â
Female
English
Short form of English Elisabeth, LIS means "God is my oath."Â
Girl/Female
American, Australian, British, Chinese, Christian, Danish, Dutch, English, Finnish, French, German, Greek, Hawaiian, Hebrew, Indian, Italian, Jamaican, Netherlands, Swedish, Swiss, Tamil
Consecrated to God; Oath of God; My God is Bountiful; God's Promise; God is My Oath
Female
Norwegian
Danish and Norwegian form of German Liese, LISE means "God is my oath."Â Compare with masculine Lise.
Female
Italian
 Short form of Italian Elisabetta, LISA means "God is my oath." Compare with another form of Lisa.
Boy/Male
Indian, Sikh
Music; In-sequence
Boy/Male
Anglo Saxon
Cunning.
Surname or Lastname
English and Scottish
English and Scottish : unexplained. Probably a shortened form of northern Irish and Scottish McLeish.
Surname or Lastname
English (East Anglia)
English (East Anglia) : metonymic occupational name for a cobbler, or perhaps a metonymic occupational name for a maker of cobblers’ lasts (see Laster).German and Jewish (Ashkenazic) : metonymic occupational name for a porter, from Middle High German last; German Last or Yiddish last ‘burden’, ‘load’.Dutch : metonymic occupational name as in 2, from Middle Dutch last ‘load’, ‘burden’; or a nickname for an awkward character, from Dutch last ‘trouble’, ‘nuisance’.French : habitational name from a place so named in Puy-de-Dôme.
Girl/Female
American, Australian, British, Danish, English, French, German, Hebrew, Swedish
God's Promise; Abbreviation of Elisabeth; My God is Bountiful; God of Plenty; Devoted to God; God is My Oath
Girl/Female
Bengali, Gujarati, Hindu, Indian, Kannada, Malayalam, Marathi, Sanskrit, Telugu
Sequence
Male
Hungarian
Hungarian form of Latin Valentinus, BÃLINT means "healthy, strong."
Girl/Female
Tamil
Anuloma | அநà¯à®²à¯‹à®®à®¾
Sequence
Anuloma | அநà¯à®²à¯‹à®®à®¾
Surname or Lastname
English
English : metonymic occupational name for a dresser of flax, from Middle English lynet, lynt ‘flax’.Dutch : from a short form of a Germanic name formed with lind (see Linde 1).Dutch : metonymic occupational name for a linen weaver or merchant.
Surname or Lastname
English (Devon and Cornwall)
English (Devon and Cornwall) : probably a variant spelling of Guest.
Surname or Lastname
Jewish
Jewish : shortened form of some Ashkenazic surname such as Littman or Litwin.English : variant of Light ‘little’.Dutch and North German : from a short form of a Germanic personal name formed with liut ‘people’, ‘tribe’ as the first element.
Male
Native American
Native American Miwok name LISE means "salmon head rising above water." Compare with feminine Lise.
Female
Hebrew
(לִי×ַתּ) Hebrew name LIAT means "you are mine."
LIST OF-SEQUENCE-ALIGNMENT-SOFTWARE
LIST OF-SEQUENCE-ALIGNMENT-SOFTWARE
LIST OF-SEQUENCE-ALIGNMENT-SOFTWARE
LIST OF-SEQUENCE-ALIGNMENT-SOFTWARE
LIST OF-SEQUENCE-ALIGNMENT-SOFTWARE
LIST OF-SEQUENCE-ALIGNMENT-SOFTWARE
LIST OF-SEQUENCE-ALIGNMENT-SOFTWARE
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