7.4. Alignment of sequence data

The alignment quality of sequences is critically important to achieving a strong phylogenetic reconstruction. There are a variety of multiple sequence alignment programs available, with varying capacity for the number of sequences input and user-determined parameter adjustments. Additionally, some aligners may be specific for protein sequence data vs. nucleotide data. Two alignment programs that are available for all computing platforms (Mac OSX, Windows, and Unix/Linux), accessible at an off-site server via the web if installing locally is not desired, and known for robust alignment algorithms are discussed here.