Perl modules for UPGMA algorithm

Santi Garcia-Vallve vallve at quimica.urv.es
Wed Mar 21 07:47:43 EST 2001

Dear Colleagues,

I want to create a web server to compare the codon usage of a group of
genes. The method that our research group has used succesfully consists in
calculating the codon usage of each gene, make a distance (derived from a
correlation coeficient) matrix for every pairwise comparisons and
constructing a dendogram using the UPGMA algorithm. Now, we use our own
FORTRAN programs and the program growtree from GCG. To do the same in a web
server I will rewritte our programs in Perl and create a CGI, but I need
some help with the UPGMA algorithm. Does anybody know where I can find a
PERL routine for the UPGMA algorithm? I have ckecked the bioperl modules
but it seems that there are not modules about constructing phylogenetic

Do you think it will be useful a web server like this?


* Dr Santi Garcia-Vallve                 *
* Bioinformatics Group                   *
* Biochemistry and Biotechnology Dept.   *
* Rovira i Virgili University            *
* Pl. Imperial Tarraco, 1                *
* 43005  Tarragona                       *
* Spain                                  *
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* telef: 34 977 559565                   *
* fax: 34 977 558232                     *
* email: vallve at quimica.urv.es           *
*                                        *
*  In the end                            *
*   We will conserve only what we love,  *
*   We will love only what we know,      *
*   We will know only what we are taught *
*                                        *
*    -Baba Dioum, Senegalese Biologist   *
*                                        *
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