Multiple Sequence Alignment
VigyanLLM's multiple sequence alignment tool uses Clustal Omega for accurate alignment of DNA, RNA, or protein sequences. The MSA engine outputs a consensus sequence, phylogenetic tree, and position-specific scoring matrices for downstream analysis.
| Input | Output |
|---|---|
| FASTA sequences | Aligned sequences with gap placement |
| Clustal/Nexus format | Consensus sequence & conservation scores |
| Distance matrix | Phylogenetic tree (Newick format) |
| Guide tree | PSSM for motif discovery |
Sequences
Alignment
Frequently Asked Questions About Multiple Sequence Alignment (MSA) Tool
Everything you need to know about using this tool
Is the MSA tool free to use?
The MSA tool offers 5 free analyses per user. After that, a subscription is required. Each alignment uses backend compute resources for accurate ClustalW/MUSCLE-based alignment.
What is multiple sequence alignment?
MSA aligns three or more biological sequences to identify conserved regions, mutations, and evolutionary relationships. It is essential for phylogenetic analysis, conserved domain discovery, and variant analysis.
How many sequences can I align at once?
You can align up to 50 sequences at a time. Longer sequences and larger datasets produce more comprehensive results.
Do I need to create an account?
No, you can use the MSA tool without an account for your first 5 analyses. Creating an account allows you to track usage and manage subscriptions.
What alignment methods are supported?
The tool supports ClustalW and MUSCLE alignment algorithms with configurable gap penalties and scoring matrices.
How do I subscribe for unlimited access?
You can subscribe through the VPrime 2.0 platform. Subscriptions start at ₹99/day for the Daily Pass with monthly plans from ₹2,499/month.