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st: Program bundle for sequence analysis

From   Ulrich Kohler <>
Subject   st: Program bundle for sequence analysis
Date   Tue, 8 Aug 2006 17:46:27 +0200

Dear all,

on behalf of my co-authors Christian Brzinsky-Fay and Magdalena Luniak I like 
to inform you, that a bundle of Stata programs (SQ-Ados) for performing 
sequence analysis has been uploaded to the SSC-Archive. The programs can be 
installed from within Stata with 

. ssc install sq

Sequences are entities build by a limited number of elements that are ordered 
in a specific way. A typical example is the human DNA, where the "Elements" 
Adenin, Cytosin, Guanin and Thymin (the "organic Bases") are ordered into a 
sequence. Other sequences are songs, that are build by tones that appear in a 
specific order, or careers of employers that are build by specific 
job-positions and ordered along time.

The SQ-Ados are a bundle of commands to describe, analyze and group the 
sequences of a sequence dataset. As it stands the following sq commands are 

   sqset             Declare data to be sequence data
   sqdes             Describe sequences
   sqtab             Tabulate sequences
   sqegen            Generate variables reflecting entire sequences
   sqstat            Describe, summarize, and tabulate sq-egenerated variables
   sqindexplot       Graph sequences as sequence index plot
   sqparcoord        Graph sequences with parallel coordinates.
   sqom              Optimal matching of sequences
   sqclusterdat      Prepare a dataset to perform Cluster analyses on the
                            results of sqom
   sqclustermat      Perform one Cluster analysis on the results of sqom

All programs are fully documented with help files. In addition -help sq- 
provides a general introduction and -help sqdemo- a software demonstration. 
An article for the Stata Journal is "in the making".

Installation note

Installation of the SQ-Ados conflicts with the older SQ-package by Nick Cox. 
Users of this package need to install the SQ-Ados with

. ssc install sq, replace

and reinstall Nicks package with

. ssc install sqr

Here is Kit Baum's explanation for breaking the rule that the first claimant 
of a name has rights to the name:

> ... There was a little problem, which was not immediately  
> apparent as you do not actually have a sq.ado. The module name SQ was  
> already in use within SSC by Nick Cox for a graph7 utility. As I did  
> not detect this problem until partway through the installation, I did  
> not follow the usual rule that the first claimant of a name has  
> rights to the name. As your package is very large and complicated,  
> and has been designed for Stata 9 with Mata components, I decided to  
> exercise the discretion to rename Nick's sq routine to sqr (it makes  
> old-style graphs square). That seemed more straightforward than  
> insisting that you rename your entire suite of routines something  
> like 'seq'; 

My apologies to Nick for taking over his name, and many thanks to Kit Baum for 
not forceing me to change the SQ-Ado bundle.

Many regards

Ulrich Kohler

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