The Flux Simulator aims at modeling RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts.
The Flux Capacitor predicts abundances for transcript molecules and alternative splicing events from RNAseq experiments. Additionally, there is a simulation pipeline that is capable to simulate whole transcriptome sequencing experiments.
T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle, etc.) into one unique alignment (M-coffee). T-Coffee can align Protein, DNA and RNA sequences. It is also able to combine sequence information with protein structural information (Expresso), profile information (PSI-Coffee) or RNA secondary structures (R-Coffee).
SymCurv is a computational ab initio method for nucleosome positioning prediction. It is based on the structural property of natural nucleosome forming sequences, to be symmetrically curved around a local minimum of curvature.
Starcode is a DNA sequence clustering software. Sequence clustering is performed by finding all pairs below a Levenshtein distance metric. Typically, a file containing a set of related DNA sequences is passed as input, jointly with a parameter specifying the desired cluster distance. Starcode aligns and computes the distance between all the sequence pairs and prints a line for each cluster containing: canonical DNA sequence, sequence count and the list of sequences that belong to the cluster.
Starcode has many applications in the field of biology, such as DNA/RNA motif recovery, barcode clustering, sequencing error recovery, etc.
sQTLseekeR is a R package to detect splicing QTLs (sQTLs), which are variants associated with change in the splicing pattern of a gene. Here, splicing patterns are modeled by the relative expression of the transcripts of a gene.
sgp2 is a program to predict genes by comparing anonymous genomic sequences from different species. It combines tblastx, a sequence similarity search program, with geneid, an ab initio gene prediction program.
