Downloads

Visit the official distribution pages to download the programs:

Multiple Alignment

• MUSCLE
• T-Coffee and 3DCoffee / Expresso
• ClustalW — Debian distribution
• ProbCons 1.12 (Debian distribution)

Phylogeny

• PhyML
• TNT official distribution — see its license agreement.
• FastME and BioNJ
• PHYLIP: Neighbor, Drawgram and Drawtree
• MrBayes
• ASTRAL

Tree Viewers

• Archaeopteryx, the successor to ATV — open your downloaded Newick or NHX tree in the desktop application.

Alignment Refinement

• Gblocks — Bioconda distribution
• Jalview

Format Conversion

• Readseq (D. Gilbert's original sequence converter)

Other programs and databases

• SMS and the ATGC scientific platform
• NCBI BLAST programs and databases

Sample data

• DNA sequences (FASTA)
• Phylogenetic tree (Newick)
• Distance matrix (PHYLIP)

The tree drawing and editing page provides SVG, PNG, PDF, PostScript and tree-format exports in your browser.