Version 8.0 for windows still has a bug with the merge.files command. Before (version7.0), it gave an error saying it couldn’t read multiple input files. Now it reads the files and combines them, but it looks like it’s leaving a strange character between the first data line of the second (and third, fourth, etc.) input file and after the last data entry in the second input file. The character is Ã¿ . This isn’t a major problem since I can use my text editor to do a find and replace to remove them. Unfortunately, it doesn’t leave a return at the end of the input files to note where the first input ends and the second begins (I’m assuming this character is supposed to be a new line symbol).
Again, you can get around this by making sure to leave a blank line at the end of each input file. I’m using it to merge multiple fasta files for individual samples (after running unique.seqs) and I’m not sure if it would cause a glitch if each sequence didn’t start on a new line (despite the “>” denoting a new sequence name).
Anyway, I just wanted to point this out since I posted about the previous bug. Please let me know if you have any advice or need additional information. Thanks.