Compare · 9 tools
Sequence search, alignment and phylogenetics tools you can run online
These tools process biological sequences, search databases, remove redundancy, build multiple sequence alignments, and infer evolutionary trees for nucleotide, protein, and structural data.
What sequence search, alignment and phylogenetics tools do
Biological sequence workflows address stages from initial sequence handling to evolutionary analysis. High-throughput sequencing generates substantial volumes of FASTA and FASTQ data that require inspection, filtering, format reformatting, and dereplication. When interrogating functional or taxonomic identity, researchers align queries against reference databases, which requires balancing search sensitivity, speed, and statistical evaluation.
For downstream comparative biology, multiple sequence alignment programs establish residue-level correspondences across homologous sequences or macro-molecular structures. These aligned matrices serve as the input for phylogenetic inference software, which applies maximum-likelihood criteria and evolutionary substitution models to reconstruct ancestral relationships and evaluate branch support.
Compared
- SeqKitSequence utilitiesA cross-platform toolkit for fast inspection, filtering, conversion, and analysis of FASTA and FASTQ files.See its pagePreinstalled
- BLAST+Sequence searchFinds regions of local similarity and calculates statistical significance across nucleotide and protein sequences.See its pagePreinstalled
- DIAMONDSequence searchAccelerated sequence aligner for comparing protein and translated DNA sequences against protein databases.See its pagePreinstalled
- MMseqs2Sequence searchSearch and cluster massive protein and nucleotide sequence sets across CPUs and GPUs.See its pagePreinstalled
- CD-HITSequence searchClusters protein and nucleotide sequences by sequence identity to eliminate redundancy.See its pagePreinstalled
- MAFFTAlignment and phylogeneticsA multiple sequence alignment program for amino acid or nucleotide sequences.See its pagePreinstalled
- MUSCLEAlignment and phylogeneticsGenerates multiple sequence alignments for proteins and nucleotides, alongside protein structure alignments.See its pagePreinstalled
- FastTreeAlignment and phylogeneticsInfers approximately-maximum-likelihood phylogenetic trees from large alignments.See its pagePreinstalled
- IQ-TREEAlignment and phylogeneticsInfers maximum-likelihood phylogenetic trees with automated model selection and ultrafast branch support.See its pagePreinstalled
How to choose
For file manipulation and sequence filtering, SeqKit provides command-line utilities for FASTA and FASTQ files across various compression formats without external dependencies. For sequence searching, BLAST+ remains standard for assessing statistical significance across nucleotide, protein, and translated databases, alongside workflows like primer design and vector screening. When searching vast protein datasets, DIAMOND offers accelerated translated and protein-to-protein alignments with frameshift tolerance for long reads. MMseqs2 handles massive nucleotide and protein datasets, searching up to 10,000 times faster than BLAST with optional GPU acceleration, and provides linear-time clustering through easy-linclust to avoid quadratic slowdowns.
For clustering by identity to eliminate redundancy, CD-HIT partitions protein or nucleotide sequences and compares distinct sequence sets via cdhit-2d and cdhit-est-2d, though it requires an external BLAST+ binary for psi-cd-hit. MMseqs2 serves as an alternative for large-scale clustering, offering both cascaded clustering and linear-time scaling, but by default estimates identity rather than computing exact identity unless explicitly instructed.
For multiple sequence alignment, MAFFT offers algorithms spanning progressive Fast Fourier Transform heuristics for large datasets to accurate iterative methods like L-INS-i for smaller collections (fewer than roughly 200 sequences and 2,000 sites). MAFFT also permits adding new sequences into pre-existing profile alignments. MUSCLE generates alignments for nucleotides and proteins, constructs alternative ensembles to quantify alignment uncertainty, and performs multiple protein structure alignments via MUSCLE-3D when paired with reseek.
For phylogenetic reconstruction, FastTree builds approximately-maximum-likelihood trees from large alignments. When full maximum-likelihood optimisation, automated substitution model testing, and rigorous branch confidence estimates are necessary, IQ-TREE incorporates ModelFinder for model and partition selection and UFBoot for rapid branch support assessment.
Questions
Can I run these tools without a GPU or installing anything?
Yes. The research agent runs each of these on a machine of its own — some are preinstalled, others are set up the first time a task needs them — and reads the results back to you.
When should DIAMOND or MMseqs2 be chosen over BLAST+ for sequence search?
BLAST+ evaluates statistical significance across nucleotide and protein databases and provides specialised utilities for primer design and vector screening. DIAMOND is tailored specifically for high-speed searches of protein and translated DNA queries against protein databases, with support for frameshift alignments in long reads. MMseqs2 searches both nucleotide and protein datasets at scales up to 10,000 times faster than BLAST, with support for GPU acceleration and profile searches.
How do MAFFT and MUSCLE compare for multiple sequence alignment?
Both programs align nucleotide and amino acid sequences. MAFFT provides a range of strategies from fast heuristics to iterative refinement methods (such as L-INS-i), and can add fragments to existing alignments without realigning the entire dataset. MUSCLE generates alternative alignment ensembles to measure uncertainty and can align protein structures using its MUSCLE-3D routine alongside the external reseek tool.
What is the operational difference between FastTree and IQ-TREE?
FastTree computes approximately-maximum-likelihood phylogenetic trees and is tailored for large alignments. IQ-TREE conducts stochastic maximum-likelihood tree searches with automated model and partition testing via ModelFinder, branch support analysis via ultrafast bootstrapping (UFBoot), and topology hypothesis tests.
Which tool should be used to cluster sequences and eliminate redundancy?
CD-HIT clusters nucleotide or protein sequences based on identity thresholds and provides specialised tools to compare two separate datasets against each other. MMseqs2 offers clustering for very large sequence sets via its cascaded clustering workflow and the linear-time easy-linclust algorithm, which scales directly with sequence count.
Written from each tool's own documentation, as summarised on its page here. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.