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. 2014 Aug 11;15(1):273. doi: 10.1186/1471-2105-15-273

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© Wang et al.; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Updated steps of SC to generate new ARG from current ARG. The same step numbers and case numbers as in the methods section are used here. Step 3 is a new type 1 recombination created on the current ARG. In step 4, the new branch coalesces into an old branch or a branch on current tree. If the new branch coalesces into the current tree, a new ARG has been constructed. If the new branch coalesces into an old branch, then there are two cases, case 5.1 and case 5.2. In case 5.2, a new ARG is generated. In case 5.1, a new branch is generated which could be dealt with in step 4. When a new ARG is generated, it turns into current ARG and a new round begins. For more details, see the Methods section.