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A new version of phylogeny.fr is available.
Please try it:
NGphylogeny.fr
.
Neighbor 3.67 (
doc
)
1. Overview
2. Data & Settings
3. Results
Datatype:
auto-select
protein
DNA
Upload your alignment (FASTA, Phylip, Clustal, EMBL or NEXUS format) or your
distance matrix
in 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 association
Optionally, 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 data
Short 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
bootstraps
In 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:
Default
Jones-Taylor-Thornton matrix (aa)
Dayhoff PAM matrix (aa)
Kimura 2 parameters (na)
Jukes-Cantor (na)
Hamming (na)
Gamma distribution parameter (for amino-acid substitution models):
Transition / transversion ratio (for nucleic acids):
