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Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. Documentations can be found at Infernal homepage
A parallel version is available. It can be used at Deimos like:
bsub -n 4 -e %J_err.txt -a openmpi mpirun.lsf cmsearch --mpi --fil-no-hmm --fil-no-qdb 12smito.cm NC_003179.fas
The idea of threading is to use an existing protein structure to model the structure of a new amino acid sequence. OpenProspect is an Open Source Protein structure threading program. You can even generate your own Protein Templates to thread sequences against. Once a sequence has been aligned to a library of template, there are tools to analysis the features of the alignments to help you pick out the best one.
Documentations can be found at OpenProspect homepage.
This is a FREE package of programs for inferring phylogenies and carrying out certain related tasks. At present it contains 31 programs, which carry out different algorithms on different kinds of data. Documentations can be found at Phylip homepage.
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Documentations can be found at PhyML homepage.