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IMAP (Integrative Meta-Assembly Pipeline)
- Chromosome-level genome assembler combining multiple de novo assemblies.
- Song et al., PLoS ONE, 2019.
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AGAPE (Automated Genome Analysis Pipeline)
- This pipeline automates the process of pan=genome analysis and encompasses assembly, annotation, and variation-calling steps.
- Song et al., PLoS ONE, 2015.
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CHAP 2 (The Cluster History Analysis Package 2)
- This is the second major release of the CHAP package for analyzing the evolutionary history of gene clusters.
- Song et al., Genome Biol. Evol., 2012.
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CHAP (The Cluster History Analysis Package)
- This software package detects conversion events and visualizes them in multiple genome sequences.
- Song et al., BMC Evol. Biol., 2011.