TREND
TRee-based Exploration of Neighborhoods and Domains
domains

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Set options

Redundancy (CD-HIT):

Alignment (Mafft):

Alignment Algorithm:

Tree Building:

A.A. Substitution Model:
Phylogeny Test:
Number of replicates:
Tree Building Method:
A.A. Substitution Model:
A.A. Substitution Model:
A.A. Substitution Rate:
Initial tree for ML:
Gaps and Missing Data:
Site Coverage Cutoff:
Phylogeny Test:
Phylogeny Test:
Number of replicates:
true

Protein Features:

Algorithm:
HMMER Databse:
E-value threshold:
Domain Score:
RPSBLAST Database: E-value threshold:

Low Complexity:
Enumerate:

Wrong format. The fasta format is expected to begin with '>' sign. To start the analysis you need to choose all the necessary files or paste the sequences in the areas. To start the analysis you need to choose a file with protein sequences or paste the sequences in the area above. There should be at least 3 protein sequences to start the analysis. You can't both provide sequences and check 'Retrieve sequences'

Full-length protein sequences go here.




Wrong format. The fasta format is expected to begin with '>' sign. There should be at least 3 protein sequences to start the analysis.

Fragments of protein sequences go here.



Protein names in the provided files should be matched.

The following combinations of the files can be provided depending on the task:

  • File with the tree + File with the alignment + File with initial protein sequences.

    Protein features will be identified and mapped on the tree, the alignment will be reordered according to the tree leaves.

  • File with the tree + File with the alignment.

    The alignment will be reordered according to the tree leaves.

  • File with the tree + File with initial protein sequences.

    Protein features will be identified and mapped on the tree.

  • Just a file with the tree. "Retrieve sequences (NCBI and MiST)" box should be checked. Protein identifiers should be placed at the beginning of proteins names on the tree (See Help).

    Corresponding proteins will be fetched from NCBI and/or MiST databases, protein features will be identified and mapped on the tree.

Wrong format. The fasta format is expected to begin with '>' sign. There should be at least 3 protein sequences to start the analysis.
Wrong format. The fasta format is expected to begin with '>' sign. There should be at least 3 protein sequences to start the analysis.
To start the analysis both a file with phylogenetic tree and a file with protein sequences and/or a file with the alignment should be provided.

Another option is to provide a file with phylogenetic tree and check "Retrieve sequences" below.

 Malformed newick tree. Please correct the tree.