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r517
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branches/ 488 (11 years ago) by duarte: T
tags/ 510 (11 years ago) by stehr: tagging version 0.9.1 for CMView 0.9.1
trunk/ 517 (11 years ago) by duarte: Changed Alignment class so that both alignment and sequence indexing are starting at 1 (before alignment indices were starting at 0). Also mapping is now done through arrays not maps. Changed all other classes using Alignment to accommodate this. NOTE: graph averaging hasn't been tested after the change
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