Biomedical Source Codes

Here is a collection of source codes that I have collected, modified, adapted, adopted or created. Most of them have some biomedical application or inspiration.

I don't mind receiving your comments, compliments, corrections or complaints, but please be warned that I will not do your damn homework.

For each package listed below, if you click on its name, you can see an expanded explanation of its purpose, a list of its contents, and copy the entire source code file, a sample calling program, or the results of running the calling program.

Available software includes:

• ALSCAL, a multidimensional scaling (MDS) program;
• ALSCAL_DATA_CONVERT, converts a simple data file to ALSCAL format;
• AS205, enumerate contingency tables;
• BAYES_BETA, simple Bayesian Statistics demonstration;
• BAYES_DICE, Bayesian dice estimation;
• BAYES_WEIGHT, Bayesian estimation of mixture PDF weights;
• BBML, Maximum Likelihood Parameter Estimation for the Beta Binomial PDF;
• BDMLIB, Bayesian estimation of weights of a Dirichlet mixture;
• DIRICHLET, maximum likelihood estimation of the parameters of a Dirichlet distribution;
• DISTANCES, convert multiple sequence alignment to distance matrix;
• FCODE, a preliminary version of a profile/sequence search code;
• GETWGT, Dirichlet mixture estimation;
• MDS, sample data for multidimensional scaling;
• MIXTURE, simulation of a Dirichlet mixture process;
• PATHWAYS, a first stab at detecting pathways;
• PCL_READ, extract the numeric data from a PCL file;
• PDB_EXTRACT, extract certain columns from certain lines of a PDB file;
• PDB_READ, read ATOM records from a PDB file;
• POP_AVE, compute time-average of CHARMM data;
• PS_GG_ALIGN, profile/sequence global gap alignment;
• PS_LG_ALIGN, profile/sequence local gap alignment;
• PS_QG_ALIGN, profile/sequence quasiglobal gap alignment;
• READ_ALIGN, convert an alignment file to PIR format;
• ROC, Receiver Operator Characteristic calculation for sequence analysis;
• SHEET, add arrows marking sheets in a protein plot;
• SPACER, performs a principal coordinate analysis;
• SPACER_DATA_CONVERT, converts a simple data file to SPACER format;
• SS_GD_ALIGN, sequence/sequence global distance alignment;
• SS_GG_ALIGN, sequence/sequence global gap alignment;
• SS_LG_ALIGN, sequence/sequence local gap alignment;
• SS_QG_ALIGN, sequence/sequence quasiglobal gap alignment;
• WIDTH, a histogram utility for CHARMM.

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