BLASTZ
Submitted by ruzhuchen on Tue, 2006-11-14 18:25.BLASTZ is a multiple sequence alignment program for the whole-genome human-mouse alignments. Blastz output can be viewed with the LAJ interactive alignment viewer, converted to traditional text alignments using LAT, or you can write a program to parse it.
EMBOSS 4.0.0 on LoP
Submitted by ruzhuchen on Tue, 2006-11-14 18:22.EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
AltiVec Enabled Applications
Submitted by katew on Tue, 2006-10-03 01:12.AltiVec Enabled Applications
hmmpfam 2.3.2 with reduced IO
Submitted by ycheng on Wed, 2006-09-13 21:26.This package is hmmpfam based on HMMER2.3.2. The improved package is designed with reduced IO overhead. Reduced IO is only implemented for serial version of hmmpfam in this package.
Related document http://www-03.ibm.com/servers/enable/site/technical/pdfs/ec5e.pdf
HMMPFAM 2.3.2 AltiVec_gen2 with reduced IO
Submitted by ycheng on Wed, 2006-09-13 21:10.This package is hmmpfam based on HMMER2.3.2-altivec_generation2 developed by Erik Lindahl. The improved package is designed with reduced IO overhead. Reduced IO is only implemented for serial version of hmmpfam in this package.
ClustalW 1.83 AltiVec version
Submitted by ycheng on Wed, 2006-09-13 19:48.ClustalW is a commonly-used bioinformatics application for identifying alignment within multiple DNA or protein sequences. This package is an AltiVec enabled version of ClustalW1.83 which has better performance and suitable for execution on JS20 and JS21 systems.
