IVDB Phylogenetic Tree Builder Help

Use multi-alignment results to build phylogenetic trees based on PHYLIP.


About Phylogenetic Tree Builder:

You can apply your WorkSet data to phylogenetic tree builder to build phylogenetic tree and to visualize their evolutionary relationships. The phylogenetic tree will be built in two steps: perform a multiple sequence alignment using MUSCLE (MUltiple Sequence Comparison by Log-Expectation), and then build the tree using PHYLIP. You can also build the tree by clicking the 'Build tree' button at the result page of the Multi-alignment. This provides you a better control of your alignment results as our Multi-alignment tool is based on ClustalW which has more parameters to be adjusted.

The input:
TThe input comes directly from your WorkSet. You can first perform a search in our database and then add the sequences of interest to your WorkSet for tree building.
 
Step 1: Multi-alignment using MUSCLE
Select the appropriate optimization method based on your input sequences:

  • Large alignments: Choose this option if you have a large number of sequences (a few thousands) to analyze, or the sequences are very long.

  • Faster speed: By using this option, you can get faster speed at a cost of losing accuracy. For large numbers of closely related sequences, this option works very well.

  • Huge alignments:  Choose this option if you have a very large number of sequences (tens of thousands), or the sequences are very very long.
  • Step 2: Build phylogenetic tree using PHYLIP
    Select the best algorithm and method for your input sequences

  • Type: The input sequence type: DNA or PROTEIN

  • Algorithm: Parsimony Method, Maximum likelihood Method, Neighbor-Joining Method or UPGMA Method

  • DNA matrix: F84, Kimura 2-parameter, Jukes-Cantor or LogDet

  • Protein matrix: Jones-Taylor-Thornton matrix, Henikoff/Tillier PMB matrix, Dayhoff PAM matrix, Kimura formula or Categories model

  • IVDB is supported by institutional grant from Beijing Institute of Genomics, CAS  Feedback