CatchAll is a new, platform-independent, user-friendly, computationally optimized software package which calculates a powerful and flexible suite of parametric models (based on current statistical research) in addition to all existing nonparametric procedures.
ACES is a workflow to query small sequences in a large set of genomes. It provides several outputs including BLAST results, a multiple sequence alignment file, a graphical fragment assembly file, and a phylogenetic tree file.
sgp2 is a program to predict genes by comparing anonymous genomic sequences from two different species. It combines tblastx, a sequence similarity search program, with geneid, an “ab initio” gene prediction program. In “assymetric” mode, genes are predicted in one sequence from one species (the target sequence), using a set of sequences (maybe only one) from the other species (the reference set). Essentially, geneid is used to predict all potential exons along the target sequence. Scores of exons are computed as log-likelihood ratios, function of the splice sites defining the exon, the coding bias in composition of the exon sequence as measured by a Markov Model of order five, and of the optimal alignment at the amino acid level between the target exon sequence and the counterpart homologous sequence in the reference set. From the set of predicted exons, the gene structure is assembled (eventually multiple genes in both strands) maximizing the sum of the scores of the assembled exons.
Saguaro (Genome-Wide) , SaguaroGW,is a program to detect signatures of selection within populations, strains, or species. It takes SNPs or nucleotides as input, and creates statistical local phylogenies for each region in the genome.