ProteinIQ for sequence alignment

Align sequences, reveal evolution   

Run Clustal Omega, MAFFT, and MMseqs2 alignments instantly. Build phylogenetic trees with FastTree. No command line required.

Join 1,200+ researchers using ProteinIQ

Clustal Omega

Clustal Omega

Industry-standard multiple sequence alignment for protein and nucleotide sequences. Handles thousands of sequences with high accuracy.

MAFFT

MAFFT

Fast and accurate multiple sequence alignment with multiple algorithms. Optimized for large-scale alignments and iterative refinement.

FastTree

FastTree

Rapid phylogenetic tree construction from sequence alignments. Builds maximum-likelihood trees for thousands of sequences in minutes.

01 — Challenges

Challenges we solve

Common obstacles researchers face and how ProteinIQ addresses them.

Align protein families to identify conserved regions
Build phylogenetic trees from sequence data
Cluster large sequence datasets efficiently
Identify evolutionary relationships between proteins

02 — Workflow

How it works

A streamlined workflow from input to results.

1

Upload Sequences

Paste or upload FASTA sequences for alignment

2

Run Alignment

Clustal Omega or MAFFT aligns your sequences

3

Build Tree

FastTree constructs phylogenetic relationships

4

Visualize & Export

View alignment, explore tree, download results

03 — Comparison

Traditional methods vs. ProteinIQ

See how we compare to traditional computational approaches.

AspectTraditionalProteinIQ
Software setupInstall multiple CLI tools and dependenciesZero installation—works in any browser
Large datasetsHours on local CPU, memory limitsCloud-scaled alignment in minutes
Workflow integrationManual file transfer between toolsSeamless alignment to tree pipeline
VisualizationSeparate viewer software requiredBuilt-in alignment and tree viewers

04 — Explore more

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Discover complementary workflows to enhance your research.

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