http://bioweb2.pasteur.fr/phylogeny/intro-en.html
http://phylemon.bioinfo.cipf.es/
Jalview
UGENE
Convert alignment formats (eg. clustalw -> MAF multiple alignment format (supported by UCSC Genome Browser, used by TBA and multiz))
http://biopython.org/wiki/Multiple_Alignment_Format
http://www.ibi.vu.nl/programs/convertalignwww/
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