Online programs

Homologous Sequences Search

• Blastall

Multiple Alignment

• MUSCLE
• T-Coffee / 3DCoffee
• ClustalW
• ProbCons

Phylogeny

• PhyML
• TNT
• BioNJ

Tree Viewers

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

Alignment Refinement

• Gblocks
• Jalview (hand editing)

Format Conversion

• Readseq
• Built-in converter