Tree and Sequence Annotator

Use this page if you have created a phylogenetic tree from a set of nucleotide sequences, and would like to identify the points at which residue changes occur. You must provide a matching set of nucleotide sequences and the tree: the server will return an updated tree containing annotations.

Paste your nucleotide sequences above in FASTA format, or select the sequence file. Sequences must be aligned, and the first sequence must be the root (or outgroup) sequence. Sequences must start and end on a codon boundary.

Paste your tree above, in Newick format, or select the tree file. Node names must exactly match the names used in the sequence definitions.

Use the fields above to control the residue numbering, for example to bring it in line with PDB file residue ids, which frequently contain omissions and insertions. You can leave all fields blank, in which case residues will be numbered from 1 with no omissions or insertions. Inserted ids can follow the PDB convention (e.g. 99A, 99B) or the IMGT convention (104.2, 104.1). Insertions are placed either before or after the ordinal id.

Optionally, enter the ranges of each CDR in the format startposition,endposition. If the ranges are entered, the analysis will include a classification of substitutions in each CDR. 'Set IMGT Defaults' will set each range according to the IMGT numbering scheme.