This page provides a list of recommended software for genomic analysis.

1. Blocks Blocks are multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. Block Searcher, Get Blocks and Block Maker are aids to detection and verification of protein sequence homology. They compare a protein or DNA sequence to a database of protein blocks, retrieve blocks, and create new blocks, respectively. You can also search the Blocks database through the mailfasta email searching program.(See below for information on mailfasta) The Blocks WWW interface and ftp archive can be found at: http://muller.fhcrc.org/blocks/
2. BMERC Local Software We maintain an ftp site at BMERC that lists local software that we developed that is available for downloading. You can download software from out public ftp site huxley.bu.edu or use the web interface at: FTP://ftp.pdb.bu.edu/ The directory BMERC contains many of our packages such as PIMA and GGREP. FTP://ftp.pdb.bu.edu/BMERC/
3. Clustalw The clustalw program is useful for creating multiple sequence alignments. You can learn more about clustalw at the web site: http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/
4. DNASTAR The DNASTAR package provides DNA & Protein Sequence Analysis for Windows and MacIntosh platforms. You can learn more about DNASTAR at their web site: http://www.dnastar.com
5. EGCG The EGCG package is a set of sequence analysis programs that supplements the GCG package. Two popular programs in this package are "prettyplot" and "prettybox", that produce boxed alignments and shaded alignments from pileup output. You can learn more about EGCG at their web site: http://www.sanger.ac.uk/Software/EGCG/
6. GCG The GCG package is a comprehensive sequence analysis package that runs on a variety of different mainframe environments under VMS, OpenVMS, Unix, and other operating systems. You can learn more about GCG at their web site: http://www.gcg.com
7. Mailfasta The mailfasta program reads a sequence file and sends a specially formatted email message to several different email servers, where it is processed. The results are emailed back. You can learn more about mailfasta and download it at the web site: http://iubio.bio.indiana.edu/Molecular-Biology/Molbio%20archive/search/
8. Molscript MolScript is a molecular graphics program that draws high quality static images of molecular structures, especially proteins. MolScript is operated using a command language rather than a graphical interface. Input consists of a PDB format molecule file and a user-written MolScript command file. Output possibilities include PostScript, Encapsulated PostScript, and a Raster3D command file. You can find out more information on molscript at the site: http://www.chemie.fu-berlin.de/chemnet/use/suppl/molscript/ and at http://cmm.info.nih.gov/modeling/guide_documents/molscript/molscript_document.html
9. Phylip The phylip package is useful for creating phylogenetic trees. You can learn more about clustalw at the web site: http://evolution.genetics.washington.edu/phylip.html
10. Rasmol The Rasmol program allows you to view and rotate protein structures. RasMol is free software for looking at molecular structures. It runs on Windows or Macintosh/PPC computers (also unix). It is very fast: rotating a protein or DNA molecule shows its 3D structure. You can find out more information about Rasmol, and download it from: http://www.umass.edu/microbio/rasmol/
11. Readseq The readseq package reformats both nucleic acid and protein sequences into various other sequence formats. It automatically detects many sequence formats, and interconverts among them. You can use a WWW version of readseq at: http://bimas.dcrt.nih.gov/molbio/readseq/ You can download readseq from: http://iubio.bio.indiana.edu/Molecular-Biology/Molbio%20archive/readseq/
12. Sculpt The Sculpt program allows you to view and edit proteins with a very nice GUI and allows you to rotate and change bond angles and see how this will change energy values on the fly. You can read more about Sculpt at: http://www.intsim.com
13. WUBlast WU-BLAST allows gapped alignments. WU-BLAST is written by Warren Gish, who helped write the original blast program. You can read more about wublast at: http://blast.wustl.edu/blast/README.html It can be downloaded from ftp://blast.wustl.edu/blast/executables The principal new features in WU-BLAST 2.0 are: * Gapped alignments are searched for, with potentially multiple regions of similarity to the query sequence being found and reported for each database sequence. Furthermore, the gapped alignment routines are integral to the database search itself -- not just a post-processing step grafted onto an old BLAST version 1.4 search -- and thus yield better sensitivity. When searching with gaps, each of the programs executes about 10% slower than its version 1.4 counterpart but generally yields more easily interpretable output and much better sensitivity. * Karlin and Altschul (1993) "Sum statistics" are used to evaluate the significance of multiple regions of similarity found between the query and a database sequence, as described by Altschul and Gish (1996).