2006-02-13 10:42:13 +01:00
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Jalview is a multiple alignment editor written in Java. It is used widely in a
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variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain
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2016-05-19 12:21:23 +02:00
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database) and is also available as a general purpose alignment editor.
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2006-02-13 10:42:13 +01:00
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2016-05-19 12:21:23 +02:00
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o Reads and writes alignments in a variety of formats
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2006-02-13 10:42:13 +01:00
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o Gaps can be inserted/deleted using the mouse.
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o Group editing (insertion deletion of gaps in groups of sequences).
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o Removal of gapped columns.
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o Align sequences using Web Services (Clustal, Muscle...)
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o Amino acid conservation analysis similar to that of AMAS.
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o Alignment sorting options (by name, tree order, percent identity, group).
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o UPGMA and NJ trees calculated and drawn based on percent identity distances.
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o Sequence clustering using principal component analysis.
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o Removal of redundant sequences.
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o Smith Waterman pairwise alignment of selected sequences.
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o Web based secondary structure prediction programs (JNet).
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o User predefined or custom colour schemes to colour alignments or groups.
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o Sequence feature retrieval and display on the alignment.
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o Print your alignment with colours and annotations.
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o Output alignments as HTML pages, images (PNG) or postscript (EPS).
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