Software
Aliview, Sequence alignment editor
MEGA, Molecular Evolutionary Genetics Analysis
Geneious, Bioinformatics Software for Sequence Data Analysis
Notepad++, text editor and source code editor
MAFFT, Multiple alignment program for amino acid or nucleotide sequences
RAxML – Randomized Axelerated Maximum Likelihood
BEAST, Bayesian analysis of molecular sequences
iTOL: Interactive Tree Of Life
Galaxy, open source, web-based platform for bioinformatics
The CIPRES Science Gateway, public resource for inference of large phylogenetic trees
Database
NCBI, The National Center for Biotechnology Information