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(Alignment of Multiple Protein Sequences) a suite of programs for protein multiple sequence alignment, pairwise alignment, statistical analysis and flexible pattern matching.
a tool to predict protein structure, function, and mutations using evolutionary sequence covariation.
implements an algorithm for large-scale multiple sequence alignments (400k proteins in 2 hours and 8BG of RAM).
is an implementation of a new algorithm, named Fastcov, to identify multiple correlated changes in biological sequences using an independent pair model followed by a tandem model of site-residue elements based on inter-restriction thinking.
an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
(Iterative Threading ASSEmbly Refinement) a hierarchical approach to protein structure and function prediction. Structural templates are first identified from the PDB by multiple threading approach LOMETS; full-length atomic models are then constructed by iterative template fragment assembly simulations. Finally, function inslights of the target are derived by threading the 3D models through protein function database BioLiP.
a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).
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