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3DCoffee 5.56 (doc)

Upload your set of sequences in FASTA, EMBL or NEXUS format from a file:

Or paste it here (load example of sequences)

Maximum number of sequences is 50 for proteins and 50 for nucleic acids.
Maximum length of sequences is 2000 for protein and 2000 for nucleic acids.

Names associationOptionally, you can specify the association between truncated taxon names (used in input data) and original long taxon names (human readable). Each short name of a line on the left will be associated to the long name of the corresponding line on the right.
Note: line numbers leading each line will be automatically removed, don't worry about them.

Short names used in input dataShort names are the names used in the input data. Usually, theses names are short and only contain valid characters (no spaces, quotes and such).
Note: a short name must be associated to one and only one long name.
Real long names (human readable)Long names are explicit taxon names with unlimited length and can contain special characters.

Advanced Settings...

Pairwise methods: Pairwise alignment methods will be used to make a pairwise alignment of all the possible pairs of sequences.
Lalign_pair: 10 best local alignments
Slow_pair: accurate global alignment
Fast_pair: fast heuristic global alignment
Clustalw_pair: ClustalW pairwise alignment
Mlalign_id_pair Mclustalw_pair Mfast_pair Mslow_pair

Additional alignment formats:
PIR Alignment
Pir Sequences (unaligned)
Score in ASCII format (text)

Print residues number:

Output order:

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