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phastCons scripts · Issue #230 · ComparativeGenomicsToolkit/hal · GitHub

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Detecting synteny among multiple genomes? · Issue #272 ...

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halPhyloPTrain.py with ancestral repeats · Issue #197 ...

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Filter species in a hal file · Issue #271 · ComparativeGenomicsToolkit ...

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hal2maf - option to exclude _MINIGRAPH_ sequences · Issue #224 ...

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hal2chain for faster halLiftover · Issue #193 ...

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halLiftover needs tests · Issue #86 · ComparativeGenomicsToolkit/hal ...

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Various build problems. · Issue #116 · ComparativeGenomicsToolkit/hal ...

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