Site-Specific Relative Evolutionary Rates · 246 days ago by Andrew Fernandes
Given a multiple sequence alignment, a phylogenetic tree, and an evolutionary model, this program calculates site-specific relative evolutionary rates.
A detailed manuscript describing its theory, implementation, and testing has been published in Oxford’s Bioinformatics (PubMed 18662926)
- Version 19 (26 August 2008)
- bRate-19.tgz [1.41MB]
- Minor bugfixes in the likelihood code
- Version 18.38M (03 January 2008)
- Initial release
My WinSCard "APDU View" Utility · 841 days ago by Andrew Fernandes
In this article there is no new information; I’m just posting a link to the archive for my Windows APDU-View utility program. It allows you to “spy” on command and data packets being sent to (and received from) a smartcard.
I have not updated it, and I don’t think it works correctly on WinXP-SP2 or later. I’ve linked to it here mainly for archival purposes.
Updating Adobe CS2 on a Mac · 842 days ago by Andrew Fernandes
Are you a software developer? Do you use OS X? Have you been frustrated by Adobe’s Creative Suite 2 (CS2) failing its updates for GoLive 8.0.1 and Illustrator 12.0.1?
There are many reported reasons for the failure of the update, and Adobe’s latest updaters are relatively bug-free. However, I still could not get my updaters to update!
It turns out that both of these updaters require Apple’s built-in version of Perl. If you’re like me, you probably had Fink’s, DarwinPorts’, or ActiveState’s Perl installed… and none of these will work if they appear in your PATH before Apple’s Perl!
The solution is to download Adobe’s updaters (or look in the download folder as Adobe tries to update itself), and execute them from the command line, making sure that Apple’s ”/usr/bin/perl” is in your PATH before any other Perl!
The reason Adobe’s updaters fail is that they use the first version of Perl found in the system path, which may or may not be Apple’s system Perl. Unfortunately, there are a couple of Apple-Perl-specific modules that that Adobe’s updaters require, packages not provided by any other Perl distribution.
Thanks to Apple’s ktrace for helping figure this out!
Gaussian Quadrature Formulae for Arbitrary Positive Measures · 842 days ago by Andrew Fernandes
Abstract
We present computational methods and subroutines to compute Gaussian quadrature integration formulas for arbitrary positive measures. For expensive integrands that can be factored into well-known forms, Gaussian quadrature schemes allow for efficient evaluation of high-accuracy and -precision numerical integrals, especially compared to general ad hoc schemes. In addition, for certain well-known density measures (the normal, gamma, log-normal, Student’s t, inverse-gamma, beta, and Fisher’s F) we present exact formulae for computing the respective quadrature scheme.
Availability
Source code is freely available online as a C-linkable ISO C++ library under a BSD-style license from fernandes.org. The library may be built using single, double, or extended precision arithmetic.
Publication
Please cite:
Fernandes, A. D. and Atchley, W. R. (2006) Gaussian Quadrature Formulae for Arbitrary Positive Measures Evolutionary Bioinformatics Online 2: 261–269. [PDF]
Download
- Version 1.1 (30 August 2006)
- GaussQR-1.1.zip [1.02MB]
- Types renamed to be more c++ friendly
- Includes universal Mac binaries (xCode 2.4)
- Version 1.0 (11 November 2005)
- GaussQR-1.0.zip [45.77KB]
- Initial release
FFTPACK Translated to Pure ISO C/C++ · 842 days ago by Andrew Fernandes
I have translated FFTPACK into Pure ISO C/C++, and made some nice additions.
- The original FFTPACK aliased integers and real numbers; I removed the aliasing.
- The original code was cleaned up significantly. Also, internal functions are all static, and return-types are consistent.
- Now single, double, and long-double (as well as arbitrary precision) computations are supported.
The distribution contains the cleaned Fortran, the ready-to-compile C and C++ code, documentation, tests, and annotated changes.
Download
- Version 1.1 (30 August 2006)
- fftpack-1.1.zip [44.02KB]
- Types renamed to be more C++ friendly
- Version 1.0 (11 November 2005)
- fftpack-1.0.zip [42.63KB]
- Initial release