Limitations for input files

The Process module deals with several input formats and sequence types, which begs the question of whether there are limitations on the type of files that can be loaded simultaneously into TriFusion.

The answer is almost none.

TriFusion was designed to capture all the details about your files automatically and to handle any combination you can throw at it. In the example below, 8 alignment files of nucleotide and protein sequences in Fasta, Nexus, Phylip and Stockholm formats are loaded simultaneously. Then, these files are easily concatenated into a single file with just a few clicks.

Moreover, defining partitions when there are multiple files and sequence types can be extremely time consuming and error prone to perform manually. That is why TriFusion handles all of that automatically. Even though we did not dealt with partitions in the above example, when you open a Nexus alignment file, you can see that the header and partitions block are correctly defined without any user intervention:

#NEXUS
Begin data;
    dimensions ntax=101 nchar=7030 ;
    format datatype=mixed(dna:1-3934,protein:3935-7030) interleave=no gap=-;

(... DATA ...)

begin mrbayes;
    charset DNAfas = 1-668;
    charset DNAnex = 669-1140;
    charset DNAphy = 1141-1808;
    charset DNAstockholm = 1809-2476;
    charset PROTEINphy = 2477-3934;
    charset PROTEINfasta = 3935-4966;
    charset PROTEINnex = 4967-5998;
    charset PROTEINstockholm = 5999-7030;
    partition part = 8: DNAfas, DNAnex, DNAphy, DNAstockholm, PROTEINphy, PROTEINfasta, PROTEINnex, PROTEINstockholm;
    set partition=part;
end;