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Based on the not-so-successful Pysimony (https://sourceforge.net/projects/pysimony/), the same determined student takes another go at the phylogenetic problem.
Javamony is invoked as follows:
java -jar Javamony.jar [input.fasta] [random / stepwise (starting tree)] [# of bootstraps] [outgroup taxon #1] [outgroup taxon #2] ...
Not meant as a competitive phylogenetic inference program, Javamony is an opportunity for me to acquire the Java language while learning to address and solve...
Boiler-plate code for bootstrapping CORBA 2.5+ applications. The goal is to create a set of cooperative services and components needed by CORBA apps. Essentially, a pre-fabricated CORBA infrastructure that facilitates component based software engineering
Aphid provides a facility for bootstrapping SSL-enabled Apache web
servers (mod_ssl) with an embedded Perl interpreter (mod_perl). Source is
downloaded from the Internet, compiled, and the resulting system is
installed in the directory you specify.
This was supposed to be an efficient way to do multi-dimensional hashtables. Unfortunately, it turned out to be much slower than just bootstrapping one hashtable onto another.