Introducing Weighbor 1.2

Weighbor has been updated to give more reliable and robust operation, plus quicker execution. The specific improvements are:

Infinite distance cut-off
To prevent overflow, distances above a high threshold (the exact threshold depends on sequence length and alphabet size, but is typically more than 25 replacements per site) are replaced by a maximum value well below where overflow problems can occur. This means that users can safely use huge number like 9999 or 1e99 to represent infinite distances.

Triangle inequality violation bug fix
The triangle inequality violation formulas have been made consistent so that violations of the triangle inequality longer cause erratic behavior. This problem was found to cause poor performance on trees with pairwise distances longer than about 2.4 substitutions per site. See our new simulation results.

Dynamic range improvement and checking
Because the weights depend exponentially on distance, in weighbor 1.0 it was easy to get weights of such different magnitudes that double precision arithmetic was insufficient to ensure the results would not be affected by roundoff error. We've implemented cutoffs to very large and very small weights. The cutoffs allow the program to use the entire range of double precision, but not to exceed it. If number of taxa and the input value of sequence length are so large that double precision is deemed insufficient to represent the range of meaningfully distinguishable weights, the program will terminate with an error.

More robust and flexible input
The input format has been generalized to allow a carriage return or tab to specify the end of a taxon name less than 10 characters long. Spaces (" ") in the first 10 characters are taken to be part of the name; names longer than 10 characters are read fully but they may not contain spaces.

Faster execution
By streamlining the innermost loop of the program, we've obtained a speed improvement of about 20%. Watch this space for subsequent even faster releases.

To obtain weighbor 1.2, see our current download page, and we plan to have a fully updated release, including other enhancements, within a week. Check this page for the latest information.

New: read about performance of Weighbor relative to FastME.

Weighbor Home Page

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