What are these Nematode Phylogenetic Trees?


(Database for the nematode branch of Assembling the Tree Of Life)

NemATOL trees description

Please Go Here to Access the Trees

What are these Nematode Phylogenetic Trees?

This link displays a nested set of phylogenetic trees inferred from all available 18s sequences as of 1 Oct.2004 that were at least 1500 bp in length (following the procedures below).

The trees are displayed in a nested set beginning with a tree based on all 678 nematodes and four outgroups. For display on the web we have collapsed the clades defined by >95% bootstrap support in a neighbor-joining analysis. These "clades" are represented by colored triangles (green for the main page) roughly proportional in size to the number of taxa they include. For each clade defined in the broader analysis, we reanalyzed the sequences within that clade from scratch beginning with the alignment (as per the original protocol). Each layer of the tree repeats these steps until terminal taxa are defined. Links to files in NemAToL.

For each tree constructed we have provided details of the parameters used (sequence statisitsics and methods used). In addition, all data-files (original Clustal alignment, trimmed alignment etc..) are also made available as downloadable files. The complete Tree file is also available and we strongly encourage additional analysis.

Updates

Although the goal is to ultimately produce very frequent updates we expect to update these tree files every 6 months. The next update will be completed July 2006.

References

1. Swofford, D.L., 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.

Specific version (for Methods section 4.0b 10)

2. Thompson,J.D., Gibson,T.J., Plewniak,F., Jeanmougin,F. and Higgins,D.G. (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 24:4876-4882.

Funded by NSF