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Javamony

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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 fundamental problems in phylogenetics. Therefore, for my own educational benefit, all code is original. Of course, there are probably a good deal of mistakes as well.

I distribute Javamony, as I did Pysimony, hoping that it will be of educational value to someone else or at least vaguely amusing.

Upcoming features will be:
- Support for Amino Acid sequences
- Support for additional file formats (e.g. Nexus)
- Multithreading
- Additional scoring methods (e.g. maximum likelihood)

Uses maximum parsimony, Reads a FASTA input file (DNA only), User-established outgroup, Random and stepwise-addition starting trees, Uses SPR (subtree pruning and regrafting) tree search, Performs bootstrapping, Outputs standard Newick format with bootstrap support and branchlengths, Draws final tree with bootstrap support

Javamony License - GNU General Public License version 3.0 (GPLv3)

Free download from Shareware Connection - Based on the not-so-successful Pysimony (https://sourceforge.

Publisher: Javamony | License: Freeware | Price: 0.00
Version: 1.0 | Size: 15 KB | Platform: Linux, Mac OS X, WinOther
Released Date: | Rating: 0 | Title: Javamony

Author Url: http://sourceforge.net/projects/javamony
Program Info Url: http://sourceforge.net/projects/javamony
Download Url: http://sourceforge.net/projects/javamony/files/latest/download?source=directory
Screenshot Url: http://sourceforge.net/projects/javamony/screenshots/screenshot.png

Javamony related downloads:

Pysimony - UPDATE: After some bug fixes, I've ditched Pysimony for Javamony: https://sourceforge.

Shareware Connection periodically updates pricing and software information of 'Javamony' from company source 'Javamony' , so some information may be slightly out-of-date. You should confirm all information before relying on it. Software piracy is theft,  Using 'Javamony' crack, password, serial numbers, registration codes, key generators is illegal and prevent future development of Javamony.

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