For my work, I usually use FASTA format for mutliple sequence alignments and Newick format for phylogenetic trees. On the downside these formats are very simple and don’t define partion blocks etc in the alignments, and don’t provide information about fonts or colors etc in the treefiles. On the plus side, the formats are very simple and almost all phylogenetic analysis programs can take them as input and write them out as output.
When I do need a more complex format, there are tools available to convert FASTA to NEXUS or other formats.
Working at the HIV Databases, where people write to us with their problems, I have found that even the very most simple formats can present a variety of problems that are trivial but often difficult to recognize and solve. For one example the “white space” characters for tabs, spaces, carriage returns, and line feeds can differ between operating systems and cause troubles. The file looks perfectly fine to the human eye but one program or another will tell you that the format is not valid (and usually give you no clue at all as to what type of problem there is).
Today, I am working with a researcher who needs to upload his published (in press) alignment and tree to TreeBase. I am not a regular Mesquite or TreeBase user, so I am getting frustrated with attempting to create the “flavor” of NEXUS file that these two programs or sites are happy with. I have reported the issues to TreeBASE at GitHub, but I also wanted to bring it up here, as an issue to consider when developing a tool or web site for broad use. It seems to me that any tool that requires a special format should provide some help with converting a standard format to the required special format.