Table 2

Minimum and maximum DFs for simulations with 200 reads from the rpoB gene family
Method RefDB size Mean read length Mean min. DF Std. dev. min. DF Mean max. DF Std. dev. max. DF
FastTree Small 100 bp 3.8e-04 1.4e-04 6.9e + 02 8.5e + 02
400 bp 8.1e-04 4.0e-04 5.3e + 02 3.9e + 02
Large 100 bp 3.9e-04 1.4e-04 4.6e + 02 3.4e + 02
400 bp 1.1e-03 7.0e-04 2.0e + 02 1.8e + 02
RAxML Small 100 bp 2.2e-06 7.8e-07 4.6e + 05 3.4e + 05
400 bp 5.7e-06 3.3e-06 3.8e + 05 2.3e + 05
Large 100 bp 2.3e-06 7.2e-07 1.2e + 05 1.5e + 05
400 bp 7.8e-06 4.2e-06 1.5e + 05 1.9e + 05
Pplacer Small 100 bp 2.3e-06 5.5e-06 5.4e + 05 4.1e + 05
400 bp 3.4e-05 3.8e-05 4.7e + 05 2.4e + 05
Large 100 bp 4.5e-06 7.6e-06 1.5e + 05 1.7e + 05
400 bp 2.3e-05 4.0e-05 2.0e + 05 2.0e + 05

Minimum and maximum DFs were orders of magnitude away from the ideal value of 1.0, indicating that the most poorly estimated branch lengths in each simulation were typically very inaccurate. Values were somewhat smaller for simulations with 50 reads (data not shown). The mean and standard deviation values of the minimum and maximum DFs are over 30 simulations for each parameter combination. Similar trends were observed for the other gene families.

Riesenfeld and Pollard

Riesenfeld and Pollard BMC Genomics 2013 14:419   doi:10.1186/1471-2164-14-419

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