If I may toot our own horn here, I think that our seqmagick tool built on Biopython is pretty nice. It does all manner of things with a very simple command line interface.
Also in the autotoot spirit, DendroPy: NEWICK, NEXUS (of various variants), FASTA, PHYLIP (of various variants), NeXML.
I have been using seqmagick a lot, and I really like this tool - it is userfriendly, fast, and offers a lot of possibilities to change/modify and play with sequences, names, format, alignments, etc. Thanks to the Matsen group!