Structural Phylogenetics

Str2Phy

Structural Phylogenetics from Protein 3D Structure using 3Di characters

Infer maximum-likelihood phylogenetic trees directly from protein 3D structures using the 3Di structural alphabet — reaching beyond the sequence twilight zone where conventional methods lose signal.

Foldseek

Encodes 3D structure into discrete 3Di characters per residue using tertiary interaction neighbourhoods

Famsa3di + trimAl

Aligns the 3Di sequences with a 3Di substitution matrix, transfers the alignment to the amino acids, and trims poorly aligned columns

IQ-TREE 2

Maximum-likelihood tree inference with ultrafast bootstrap (1000 replicates), SH-aLRT, and the 3Di substitution model

Structures PDB AlphaFold

One per line (spaces, commas and semicolons also work). PDB: XXXX_CHAIN, for example 1hv4_A. AlphaFold: a UniProt accession, for example P69905. The order of your list is the order of the sequences in the alignment.

0 entries

0 / 53 structures (at least 4)

Step 1 builds the structural alignment. In step 2 you choose one analysis to run on it. Maximum 53 structures per job. PDB structures are fetched from RCSB and AlphaFold structures from EBI AlphaFold DB (v6) at runtime.

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