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Method: Accurate reconstruction of bacterial pan- and core genomes with PEPPAN
- Zhemin Zhou,
- Jane Charlesworth,
- and Mark Achtman
Genome Res. November 2020 30: 1667-1679; Published in Advance October 14, 2020, doi:10.1101/gr.260828.120
...core and overestimating the overall size of the pan.The second problem in computing a pan is that of differentiating orthologous genes, which have evolved by vertical descent, from paralogous genes derived from gene duplications or HGT events. Paralogous genes can become fixed in populations, but many...
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LETTER: Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events
- Olga Zhaxybayeva,
- J. Peter Gogarten,
- Robert L. Charlebois,
- W. Ford Doolittle,
- and R. Thane Papke
Genome Res. September 2006 16: 1099-1108; Published in Advance August 9, 2006, doi:10.1101/gr.5322306
.... ↵ Charlebois R.L. , Doolittle W.F. ( 2004 ) Computing prokaryotic gene ubiquity: Rescuing the core from extinction . Genome Res. 14 : 2469 – 2477 . ↵ Chase P. ( 1970 ) Algorithm 382: Combinations of M out of N objects [G6] Commun. ACM 13 , 368 . ↵ Chisholm S.W. , Olson R.J. , Zettler E.R. , Goericke R...

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