You may already be familiar with my shameless love for the Geneious Pro software. My lab uses this software to view and annotate trace files, assemble contigs, and make alignments. For these purposes, Geneious is superior to Sequencher and available for only a fraction of the price ($249 for students/$495 for other academics). What's more, the folks at Geneious are constantly making improvements. Some really cool ones are making their debut in the latest beta release (v 4.6). My personal favorite is the automated assembly function, which can be used to automatically generate contigs from sequences that share some common motif in their file names (e.g., species1_forward & species1_reverse). We're using this function to put together forward and reverse reads from short DNA fragments. Another major shortcoming of Geneious bites the dust... Of course, there are still some bugs to be worked out (we are, for example, having problems automating end trimming and assembly of sets of sequences >40), but the folks at Geneious are actively working to solve these problems.
Dechronization is authored by evolutionary biologists interested in the development and application of methods for estimating phylogeny and making phylogeny-based inferences. The goal of the blog is to provide a forum for discussion of the latest research and methods, while also providing anecdotes, tidbits of natural history, and other related information.