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While these issues have been raised previously [e.g.], [ 14], [40], [41], [42], [43], [44,45], such analyses are becoming increasingly commonplace, especially with the advent of next-generation DNA sequencing platforms and the rapid increase in genomic data, yet, many researchers appear not to consider the estimation of molecular sequence alignment as an exploratory phase of data analysis [46].
Partitioning of the molecular sequence alignment may impact on divergence time estimates [ 56, 57].
The molecular sequence alignment and trees with fossil calibrations have been deposited in Figshare: http://dx.doi.org/10.6084/m9.figshare.org/10.6084/m9.figshare
The posterior estimates of times are then the result of combining the prior (the fossil information) with the likelihood of the data (the molecular sequence alignment).
Similar(56)
The presence of gaps in molecular sequence alignments is common-place in the literature.
TS carried out the molecular sequence alignments and analyses, and the fossil review.
Phylogenetic studies based on molecular sequence alignments are expected to become more accurate as the number of sites in the alignments increases.
Researchers commonly remove gaps from molecular sequences alignments by coding them as missing data or by throwing out columns that contain gaps [ 3- 6].
Correlated mutations were obtained for intra- and inter-molecular sequence alignments using CAPS (see Methods).
JMS participated in molecular cloning, sequence alignment and immunoassay.
None declared L. Smythe conducted the molecular studies, sequence alignments and the culture of bacterial species, and participated significantly in the writing and reviews of the manuscript.
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