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Software

Sequence Analysis and Alignment

4Peaks - a very clean, user-friendly sequence analysis program for OS X.

Se-Al - a simple program for hand alignment of dna and protein sequence for OS X.

ClustalW - a web-based version of ClustalW for automated alignment of dna or protein data. I find using this web version much easier than running the software locally.

TranAlign - a web-based program to drive a nucleotide alignment based on the coding protein. Incredibly helpful. Part of the EMBOSS package.

Sequence Organization

Genome Workbench - Have not used this one, so I can't vouch for the quality or ease of use, but this is NCBI's own program for interfacing with NCBI databases. Most likely pretty cool. For OS X, Windows, Unix, Linux.

CLC Free Workbench - A solid (and very free) program for keeping track of large number of sequences. Interfaces with the NCBI database. Worth a shot. For OS X, Windows, Unix.

Phylogenetics

Joe Felsenstein's Website - the ultimate and most up-to-date resource for all software and servers phylogenetic.

PAUP* - The standard, multi-method (Distance, Parsimony and Maximum Likelihood) program used for phylogenetic inference. You can download a free trial for a bunch of different platforms, or buy the Beta version (yup, still Beta for some reason).

PHYLIP - A collection of programs written by Felsenstein for a wide variety of phylogenetic analyses.

SplitsTree4 - a fantastic program for inferring evolutionary networks. For OS X.

MrBayes - my personal favorite for inferring bayesian trees from molecular and/or morphological data. For OS X.

SIMMAP - a program for post-tree character mapping, works hand-in-hand with MrBayes. For OS X.

Primer Design

Primer3 - parameter rich web-based primer design

CODEHOP - web-based program for degenerate primer design

Molecular Evolution

K-Estimator - infers Ka/Ks ratios via a sliding window. Also generates MCMC confidence intervals. For PC.

PAML - the gold-standard suite of programs for phylogenetic sequence analysis based on maximum likelihood. For OS X, Windows, Unix.

Programming Aides

BBEdit - An absolute must word processor for the programmer. Syntax analysis and color coorination... what more could the obsessive compulsive want? Download a trial to get you hooked, pay later for the whole thang. For OS X.

Graphic Design

Omnigraffle - An easy to use and effective program for laying out posters, presentations, whatever. So much better than powerpoint, it's disgusting. You can download free trials. For OS X.