What does POWER Do?

PhylOgenetic WEb Repeater (POWER), a web-based service, is designed to perform phylogenetic analysis of proteins and DNA sequences.

The process starts with a multiple sequence alignment and builds a dendrogram based on well-established methods, ClustalW and PHYLIP. With a succinct interface for sequence input, one can draw the tree effortlessly using the default setting or with fewer modification on parameters.

When fine-tuning is needed, user can repeat easily with adding or deleting sequences of previous job.

 

Input Format

Input data of POWER includes "E-Mail", "Job ID", "Sequence" and "Job Note". The information of them are described below:

Input data Description
E-Mail
Instead of real-time manipulation, POWER preceds all the computational tasks in background and notified of its completion by e-mail to users. Therefore, e-mail address is necessary to POWER.
Job ID
This information make recognition among results easily if users perform more than one analysis with POWER.
Input Sequences in FASTA format

The FASTA sequences format consists of a sequence identifier which is recognized by a > character and the sequence in standard one-letter symbols.

See example

Symbols allowed in nucleic acid sequence

Symbols allowed in protein sequence

Input Aligned Sequences in PHYLIP input format

To the aligned sequences, POWER only allows them in PHYLIP input format, which can be generated or transfered by ClustalW. The first line of this kind of input data contains the number of species and the number of characters, in free format, separated by blanks. The information for each species follows, starting with a ten-character species name (which can include punctuation marks and blanks), and continuing with the characters for that species. The characters are each a single letter or digit, sometimes separated by blanks. (This paragraph is digested from from the documents attached with the original programs of PHYLIP)

See example

Symbols allowed in nucleic acid sequence

Symbols allowed in protein sequence

Job Note Write any information you want here.

 

Multiple Sequence Alignment Options

The options information of POWER are digested from the documents attached with the original programs of ClustalW, though have been modified very slightly to fit the design of our server.

Multiple alignments are carried out in 3 stages:

  1. Pairwise alignments: all sequences are compared to each other.
  2. Dendrogram construction: a dendrogram (like a phylogenetic tree) is constructed, describing the approximate groupings of the sequences by similarity.
  3. Multiple aglinment: the final multiple alignment is carried out, using the dendrogram as a guide.

In the stage of pairwise alignment, a distance is calculated between every pair of sequences and these are used to construct the dendrogram which guides the final multiple alignment. The scores are calculated from separate pairwise alignments. These can be calculated using 2 methods: dynamic programming (slow but accurate) or by the method of Wilbur and Lipman (extremely fast but approximate).

Phylogeny Inference Options

The options information of POWER are digested from the documents attached with the original programs of PHYLIP, though have been modified very slightly to fit the design of our server.

Related Links

 

 

 

 

 

 

 

 

 

 

 

 

 

 


© 2005 Division of Biostatistics and Bioinformatics 

National Health Research Institutes. All rights reserved. 

Lasted updated 2005/04/07