karl's bookmarks: Soft

• CODE bioFOX - "Code bioFOX aims at implementing various bioinformatics tools as an extension on the Firefox browser."
• Chimera - "UCSF Chimera is a highly extensible, interactive molecular graphics program. It is the successor to UCSF Midas and MidasPlus; however, it has been completely redesigned to maximize extensibility and leverage advances in hardware. UCSF Chimera can be downloaded free of charge for academic, government, non-profit, and personal use. It includes full user documentation and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix. UCSF Chimera development is funded by the NIH National Center for Research Resources (grant P41-RR01081)."
• EisenLab
• Information about sim4
• Open source Clustering software - "The open source clustering software available here contains clustering routines that can be used to analyze gene expression data. Routines for hierarchical (pairwise simple, complete, average, and centroid linkage) clustering, k-means and k-medians clustering, and 2D self-organizing maps are included."
• Debian-Bioinformatics
• Debian-Bioinformatics ; EMBOSS packages - deb http://debian.bioinformatics.unsw.edu.au/ unstable main
• Debian-Med: Molecular Biology and Medical Genetics
• DebianScienceBiology - Debian Wiki
• EMBOSS Homepage
• wEMBOSS Portal - Welcome to wEMBOSS
• ESSA RNA SOFTWARE HOME PAGE
• FamilyJewels: tools for comparative sequence analysis
• gbrowse_img - CGI script to generate genome images via the Generic Genome Browser
• Gist 2.1.1 - Gist contains software tools for support vector machine classification and for kernel principal components analysis.
• Matrix2png - Matrix2png is a simple but powerful program for making visualizations of microarray data and many other data types. It generates PNG formatted images from text files of data.
• MBI: Oligo Primer Analysis Software, Primer Design - The famous oligo software (non-free).
• mekentosj.com | 4Peaks - For Peaks, Four Peaks. - A really beautiful trace viewer for osX. Shame it is non-free...
• Bioinformatics.org: Molecular Linux
• mRNA Abundance Home Page
• REPuter at GENOMES.DE
• SA National Bioinformatics Institute
• Software Tools - The Institute for Genomic Research
• stackPACK v2.2
• MAFFT - a multiple sequence alignment program
• Moeller's debian packages - including primer3
• ht_utils source - A few perl scripts that I've written
• Lightweight Image Database for Labs - sourcecode - Released under the GPL
• FamilyJewels: comparative sequence analysis.
• scripts for putting up a web-based blast server - These are example cgi perl scripts for putting up a web-based blast server.
• mkdom/Xdom
• TeXshade - A LaTeX package for setting nucleotide and peptide alignments
• GMOD Modular Schema - Chado
• SBML.org - The home site for the Systems Biology Markup Language
• STRAP - multiple sequence alignment: Interactive Editor
• Gene Ontology Consortium
• The Human Gene Expression VOCabulary

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