There are many file formats for storing sequence alignments. I am trying to figure out which is the most frequently used file format for storing an alignment and associated annotations such as features, taxa sets and character sets. Imagine having an alignment of multiple genomes from two different locations, each genome having multiple genes and features specific to certain genomes. Which alignment file format would be best to store all this information and to be sure that a reasonable number of software programs would be able to interpret the information?m
I have listed as responses all the different file formats I could think of that store sequence alignments. Please vote for the ones you use the most and find the most useful. Please add any additional alignment file formats I haven't thought of.
PS: We really need a polling option in biostar because it occurs to me that people are probably not going to vote for any of these options.
PPS: Anybody have any ideas on how I can get feedback from the bioinformatics community on this question?