I am including this week a list of bioinformatics or general use software that I review and currently use. Stay tuned. (All opinions on this page are my own. I am not affiliated, nor develop any of the software cited here)
Best freely availabe phylogenetics package:
Phylip
Besides being free and open source, Phylip has more features than PAUP or any other phylogenetic package available. As a matter of fact PAUP takes 3x more time to complete a bootstrap run than Phylip. The only problem I can mention is the interface (or lack of). PAUP in my opinion would come secon, especially because of the slow update cycle and the current lack of an interface at all.
Software of choice for Bayesian phylogenetic inference:
MrBayes 3.01
The latest version of this wonderful program has improvements in its parallel implemetation. Running in large clusters is a breeze.
Sequence alignment (proteins):
Mafft
This program is developed by ... and presented the best results in a paper we published last year. Mafft had the best alignment scores, in simulated and real protein sequences. The program has many options to align sequences and has also a fast algorithm implementation. My choice of Mafft is more based on its speed connected to its quality, as ProbCons sometimes resulted in even better protein alignments, but is not as fast as Mafft.
Sequence alignment (DNA/RNA): coming soon
Best overall bioinformatics platform:
Geneious
This is what I consider the Holy Grail of bioinformatics/phylogeny/molecular biology). Geneious can do sequence alignment (although simple, extremely handy) and the better part it can help you edit your alignment, add new sequences, download from NCBI and even help you with the references for your next paper.
click for the review 1 and review 2
