Upload a New Tree
Tree
Tree Name
Upload Tree File in Newick/ETE Format
Or use an example:
Example Tree
Tree Parser
Name
Support
Is uploaded tree annotated
Metadata (Optional)
Metadata File(s)
Or use example metadata:
Example Metadata
Metadata Separator
Specify the metadata file separator (default is "<tab>", for comma use ",").
Parsing metadata
Detected Column Types:
Column
Data Type
Summary Method for Ancestor Nodes
Data Matrix (Optional)
Matrix File(s)
Matrix Separator
Specify the matrix file separator (default is "<tab>", for comma use ",").
Parsing Matrix
Detected Matrix Summary:
File Name
Data Type
Internal Numerical Representation
Taxonomic Annotation (Optional)
Activate Taxonomic Annotation
Taxonomic ID Column
name
Taxa DB
NCBI
GTDB
mOTUs
Version
-
Species Field Delimiter
Species Field Index
ignore unclassified
False
True
Species Overlap Threshold
Set the threshold for species overlap (default is 0.0).
Ancestral Character Reconstruction (Optional)
Activate Ancestral Character Reconstruction
Select ACR Column
ACR Method
(Datatype aligned with the metadata setting)
Maximum Likelihood: MPPA
Maximum Likelihood: MAP
Maximum Likelihood: ML
Maximum Parsimony: ACCTRAN
Maximum Parsimony: DELTRAN
Maximum Parsimony: DOWNPASS
Maximum Parsimony: MP
Maximum Likelihood
Bayesian
Model of Evolution
F81 (Felsenstein 1981)
Jukes-Cantor
EFT (estimate-from-tips)
BM (Brownian Motion)
OU (Ornstein-Uhlenbeck)
Phylogenetic Signal Testing
(Only available for Maximum Likelihood methods)
-
Delta Statistic
Ent-type
Shannon Entropy (SE)
Linear Shannon Entropy (LSE)
Gini Impurity
Iterations
Lambda0
Standard Deviation (SE)
Thin
Burn
Lineage specificity (Optional)
Activate Lineage specificity analysis
Select LS Column
Percision
Sensitivity
Alignment (Optional)
Alignment File
Consensus Sequence Threshold
If consensus cutff is 0, it means no consensus sequences will be computed in Ancestor nodes.
EggNOG-mapper Annotation(Optional)
Emapper Annotation
Pfam Annotation from emapper (Optional)
Pfam annotation
Annotate and Visualize Tree!
EggNOG Annotation Example
GTDB Tree Example