December 2010 Archives

I haven’t been keeping up with my Calix Cari polls this year for collage football. But now that the regular season has ended, I have found time to produce one. The events of this season have been rather unpredictable. Of course by the end of the season there were few surprises. Auburn appeared out of nowhere to become #1 on the strength of a once-in-a-decade player who fit perfectly into their offensive system. (Yay, for the booster who had cash to spare in this economy. We will see if their season stands the test of time.) But in my calculation Auburn is only #3, behind Oregon and ¡Stanford! (I still think Harbaugh would make a smooth transition into the coach’s chair at UGA but wouldn’t be there long. It’s good that Richt was retained.)

It appears my algorithm likes the Pac-10 over the SEC, and Auburn lost ground because of its tight victories, early in the season.

6Boise St11-16.8977
8Ohio State11-16.5913
9Texas A&M9-36.5043
10Oklahoma St10-26.4876

Ngila 1.3 Released

It has been a long time coming, but I have finally released Ngila 1.3. This version fixes a few bugs and includes many new features.

  • Use CMake for compilation and installation
  • New scaling option enabled by default (identical sequences default to cost of 0)
  • Protein evolutionary models: aazeta and aageo
  • Fasta and Phylip format output support
  • Clustal and Phylip format input support
  • Report sequence identity measure
  • Matrix output formats for distance measures
  • Look for “ngilarc” file in the home directory.
  • New separator option
  • New const-align option
  • Replace arg-file option with ngilarc option.
  • Use custom zeta function if GSL not found.
  • Optimize size of travel table.
  • Ordering of –pairs-all fixed
  • bug fix for output of large alignments >10kb
  • minor bug fix for geo model

About this Archive

This page is an archive of entries from December 2010 listed from newest to oldest.

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