Twine is a Java GUI with multiple graphical representations (‘Views’) of enhancer alignments that displays motifs, as IUPAC consensus sequences or position frequency matrices, in the context of phylogenetic conservation to facilitate cis-regulatory element discovery.
MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.
CNCI (Coding-Non-Coding Index) is a powerful signature tool by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations.
BASELINe, a new computational framework for Bayesian estimation of Antigen-driven selection in Immunoglobulin sequences, provides a more intuitive means of analyzing selection by actually quantifying it.
Biogrep is a tool designed to quickly match large sets of patterns against biosequence databases and is optimized for multi–processor computers. Biogrep uses standard POSIX extended regular expressions and can divide the pattern–matching task between a user–specified number of processors.
Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution.