Tigr Assembler v2/Scan
Submitted by boogles on Thu, 2006-08-31 21:26.The TIGR Assembler is the classic assembly tool developed by TIGR to build a consensus sequence from smaller sequence fragments. TIGR Assembler is comparable to Phrap and other greedy algorithm based assemblers.
PHYLIP
Submitted by boogles on Thu, 2006-08-31 21:23.PHYLIP is a free package of programs for inferring phylogenies.
Hmmer 2.3.2 IBM JS20 Suse
Submitted by boogles on Thu, 2006-08-31 21:18."Profile hidden Markov models can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.The advantage of using HMMS is that HMMS have a formal probabilistic basis and can be trained from unaligned sequences, if a trusted alignment isn't yet known. They do however make poor models of RNAs because they cannot describe base pairs. HMMER is a freely distibutable implementation of profile HMM software for protein sequence analysis. (Washington Univ.)"
Genesplicer SLE9
Submitted by boogles on Thu, 2006-08-31 21:16."A fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice. It was compared to six programs representing the leading splice site detectors for Arabidopsis thaliana and Human: NetPlantGene,NetGene,HSPL,NNSplice,GENIO and SpliceView. In each case GeneSplicer performed comparably to the best alternative,in terms of both accuracy and computational efficiency."
