The following software packages are available. Please, refer to the included readme files and the corresponding publications for additional information. Most of these packages have been developed under a Linux environment.
This is a program to detect and evaluate the presence of chimeras and cross-over recombination in sequence data. This program and procedure has been described by Gonzalez et al. (2005; Evaluating putative chimeric sequences from PCR amplified products and other cross-over events. Bioinformatics 21: 333-337).
There are versions to be downloaded for the Linux and Windows operating systems. For the Unix/Linux operating systems you should download the file ccode25.tar and for the Windows/DOS operating systems you should download the file ccode025w.exe (windows version). To align the selected sequences you can use ClustalW or some other program. If you use ClustalW, the right version needs to be installed. Below, please, find links to an UNIX/Linux version as well as to Windows/DOS (not XP or above) and Windows XP versions.
Ccode for UNIX/Linux. Tar file containing: ccode025 executable (Linux Red Hat v. 9.0), ccode025.c (source code), Readme.1st (manual; text file) and run_ccode025 (a shell script requiring clustalw).
Ccode for windows/dos. Zip file containing an executable ccode025 version for windows/dos platforms and some brief installation instructions.
ClustalW 1.83 for UNIX. Compressed (tar) file containing clustalW1.83 for Unix (including Linux).
ClustalW 1.83 for DOS and Windows (excluding XP and above). Compressed (zip) file containing clustalW1.83 for Windows/DOS platforms (excluding Windows XP).
ClustalW 1.83 for Windows XP. Compressed (zip) file containing clustalW1.83 only for the Windows XP operating system.
We are preparing a program (Blent) to automatize the process of searching for homologue sequences to a query (using Blast and Entrez at NCBI), alignment (using ClustalW), and chimera detection (using Ccode). When ready, this improvement will allow quick and automated analysis of sequences.
This program allows to compare pairs of communities and determines if they show significant differences. It was originally proposed to differentiate microbial communities based on molecular profiles or fingerprints as described by Portillo and Gonzalez (2008; Statistical differences between molecular fingerprints from microbial communities. Antonie van Leeuwenhoek 94: 157-163). Fingshuf was developed under the Linux operating system and can be downloaded here. (fingshuf.zip)
This program finds repeated sequences or motifs in DNA fragments and genomes. It was written in C under the Linux operating system. It was reproted in Portillo and Gonzalez (2009; CRISPR-elements in the Thermococcales: evidence of associated horizontal gene transfer in Pyrococcus furiosus. Journal of Applied Genetics 50: 421-430). Fires can be downloaded here. (fires03.zip)
This is a program to perform counts using the Most Probable Number (MPN) procedure. It is useful to obtain complete MPN tables for any desired number of dilutions, tubes, and different amounts of samples, as well as to estimate the MPN for a single experiment. The program has been described by Gonzalez (1996; A general purpose program for obtaining Most Probable Number tables. Journal of Microbiological Methods 26: 215-218). This program was written for the DOS operating system although in works under any MS Windows version using the command line option. It can be downloaded here. (mpn4.zip)