The idea of bioshell is to extends Linux command line by commands for manipulating bioinformatics data. In the current version the following programs are provided:
- acorr - calculates autocorrelations based on given scalar and vector - type observables
- hist - prepares 1D and 2D histograms
- seqc - converts between sequence formats, such as FASTA, PIR, SEQ; also extracts sequences from PDB. Sequences can be sorted and/or filtered by this tool.
- clust - hierarchical clustering of various data, e.g. protein models (originaly published as ‘HCPM’)
- strc - structure converter utility, e.g. extracts chains from PDB
- str_calc - basic calculations on biomolecular structures. Evaluates angles, distances, contact maps, hydrogen bonds etc.
- trac - converts trajectories computed by CABS / SURPASS protein modeling software
- blast_analyse - analyses multiple output files from PsiBlast
- seq_align - calculates alignments between sequences and sequence profiles