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
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;
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
Input file types: fasta, meg (Lasergene), msf
Alignment programs: ClustalW
Output: meg, save as msf, nex
