Home
Phylogeny Analysis
"One Click"
"Advanced"
"A la Carte"
Blast Explorer
Online Programs
Blast
Blast
Multiple Alignment
MUSCLE
T-Coffee
ClustalW
ProbCons
Phylogeny
PhyML
BioNJ
TNT
MrBayes
Tree Viewers
TreeDyn
Drawgram
Drawtree
ATV
Utilities
Gblocks
Jalview
Readseq
Format converter
Your Workspace
Documentation
Downloads
Contacts
BioNJ (
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, no parameter is used
(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: 5000;
Limits for nucleic acids: max. sequences = 5000, max. length = 5000;
Limits for proteins: max. sequences = 5000, max. length = 5000.
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 BioNJ 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 (protein)
Dayhoff PAM matrix (protein)
Kimura 2 parameters (DNA/RNA)
Jukes-Cantor (DNA/RNA)
Hamming (DNA/RNA)
Gamma distribution parameter (for amino-acid substitution models):
Transition / transversion ratio (for nucleic acids):