Online programs

Run an individual analysis or combine processing steps in A la Carte.

Homologous Sequences Search

• BLAST — Swiss-Prot or your own database; additional databases at NCBI BLAST.

Multiple Alignment

• MUSCLE
• T-Coffee / 3DCoffee / Expresso
• ClustalW
• ProbCons
• MAFFT
• Clustal Omega

Phylogeny

• PhyML
• TNT
• BioNJ
• MrBayes
• Neighbor
• FastME
• ASTRAL
• IQ-TREE 3
• RAxML-NG
• FastTree

Tree Viewers

• TreeDyn
• Drawgram
• Drawtree
• ATV (A Tree Viewer)
• Reactree

Alignment Refinement

• Gblocks
• Jalview (hand editing)
• Built-in Curer
• BMGE
• ClipKit
• ReSeqt (alignment viewer)

Format Conversion

• Readseq
• Built-in converter

Model Selection

• SMS