Cote Laboratory
  • Research
    • Cyclic nucleotides as second messengers
    • The PDE superfamily
    • Central role of PDE6 during visual signaling
    • Molecular pharmacology of PDEs
    • PDEs in nematodes
  • People
    • Contact Us
    • Cote lab group photos 1994-present
    • Cote Lab Alumni
    • Undergrad research awards 1988-present
  • Publications
  • Academics/UNH
  • Protein Bioinformatics Resources
    • Protein databases
    • Multiple Sequence Alignment
    • Phylogenetics
    • Protein Structure
    • Protein Evolution
  • Cotelab portal

Sequence Alignment Programs

Jalview 2.8.2 (Java desktop application)

Performs multiple sequence alignments, visualisation (coloring, consensus logo), and analysis. Particularly useful for editing sequence alignments, as well as generating  phylogenetic trees and principal components analysis (PCA) plots.
Input: fasta, msf, phy, Jalview project files
Alignment programs: ClustalO , MAFFT, MUSCLE, TCoffee, Probcons
Tree-building programs: Neighbor-Joining, Average Distance
Output: same as input 
Export: image file types include jpg and png

Megalign Pro (Lasergene)

User-friendly multiple sequence alignment program, but in its native format generates msa files that are not readable by other programs.
Input file types: fasta, msa (Lasergene)
Alignment programs: ClustalO, MAFFT and MUSCLE
Output: save alignment as msf, fasta, nex file formats 
Export: Send alignment to Megalign; Send tree to FigTree; 

Megalign (Lasergene)

Not the best choice for performing alignments (uses Clustal W) but useful for generating alignment reports.
Input file types: fasta, meg (Lasergene), msf
Alignment programs: ClustalW
Output: meg, save as msf, nex

Picture