Gontang, Fenical and Jensen used Clusterer to analyse data in manuscript Phylogenetic Diversity of Gram-Positive Bacteria Cultured from Marine Sediments.

Documentation for ClustalW, a general purpose multiple alignment program for DNA or proteins, is posted on Bugaco .com bioinformatic's documentation section.

New Nexus to Mega converter is available at Bugaco's bioinf section. Tools allows user to copy/paste data to online form and perform easy conversion from Nexus to Mega format.

New Nexus to Fasta converter is available at Bugaco's bioinf section. Tools allows user to copy/paste data to online form and perform easy conversion from Nexus to FASTA format.

Clusterer manuscript has been published at: Klepac-Ceraj V, Ceraj I, Polz MF Clusterer: extendable java application for sequence grouping and cluster analyses, Online Journal of Bioinformatics, 7 (1) : 15-21, 2006.
Clusterer is available at Polz website

Clusterer now supports NEXUS and FASTA as input file formats. Clusterer supported FASTA format from its inception, NEXUS format is more complex and due to development constrains was not added to initial release.
NEXUS file format is added to the Clusterer to help its faster adoption.

Chimera Buster, novel algorithm for finding putative chimerical sequences in clone libraries with high coverage is acknowledged in Vanja’s article. Article appeared in Environmental Microbiology under title "High overall diversity and dominance of microdiverse relationships in salt marsh sulphate-reducing bacteria".

Quote from the article: “The data were also checked for putative chimeras by the RDP Chimera_Check (Maidak et al., 1999) and the ChimeraBuster algorithm, which was newly developed to specifically analyze clone libraries with high coverage.”

I discovered today some issues with Java 2 v1.3. They are related to Swing (User Interface) methods new to JDK 1.4.
Please use Java 2 v1.4 until this issues are resolved.
"Open local file" feature is added, to make it easier to paste fasta file into Clusterer.
Thanks,
Ivan

New design and layout of bioinformatics @ bugaco.com is underway. New look & feel should allow easier and clearer navigation on the site.
Most of the redesign should be done by mid February.

Linebreaker applet is new applet posted on bioinformatics @ bugaco. Tool provides an UI for conversion between line break formats used by UNIX, Machintosh and Windows. To start this tool use click here. This tool will get its place on menu bar soon.

Dear Visitor,
Blog is added to bioinformatics @ bugaco.com to help better understand user community, to get feedback about tools, and to get fresh ideas how to improve user experience with tools provided.