Neighbor 3.67 (doc)




Datatype: auto-select       protein       DNA

Upload your alignment (FASTA, Phylip, Clustal, EMBL or NEXUS format) or your distance matrixin case of a distance matrix, parameters are ignored (Phylip or NEXUS format) from a file:

Or paste it here (load an example of alignment or an example of distance matrix)

Maximum number of taxa for a distance matrix: 500;
Limits for nucleic acids: max. sequences = 5000, max. length = 5000;
Limits for proteins: max. sequences = 5000, max. length = 5000.

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.



Settings


Number of bootstrapsIn the case of a protein analysis, realised by combining Seqboot (Phylip package) to perform bootstrap and Consense (Phylip package) to obtain the bootstrap tree from the Neighbor output (limit=1000). In the case of a nucleic acid analysis, realised by FastDist, and consensus generated by Consense (Phylip package) (limit=1000).:

Substitution model:   


Gamma distribution parameter (for amino-acid substitution models):    

Transition / transversion ratio (for nucleic acids):    




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