Adjust verifycmd for MUSCLE

Without any command-line arguments, the behavior and exit code of the MUSCLE executable
depend on whether isatty(stdin). If that's not the case (as in certain unattended
environments, but evidently not Travis), it'll try to read from stdin and fail. Very
nasty to debug because it then works as expected when you try it interactively! Running
with -version is more predictable.
read_utils.py purge_unmated: add an argument to customize the regex used to parse paired read IDs
in the FASTQ files. Helpful for files generated by SRA fastq-dump, which emits read IDs formatted
differently from the Illumina base caller.