IntroductionPhylogenies, tree diagrams that represent evolutionary relationships among species (or taxa, more generically), are often estimated from molecular sequences. This estimation process typically occurs in two distinct steps. First, molecular sequences are aligned into a matrix (called an alignment), possibly by adding gap characters within sequences to account for historical insertions and deletions (indels) of nucleotide bases. Second, the phylogeny is estimated from the previously estimated alignment. This sequential approach ignores alignment uncertainty, leading to several problems with phylogenetic inference.If the alignment contains ambiguous regions, ignoring uncertainty in the alignment can result in exaggerated support for inferred phylogenies (Lutzoni et al., ). Moreover, if the sequence alignment is determined by an alignment method that assumes a fixed guide tree, then the estimated phylogenies in the second step may be biased toward this fixed guide tree (Nelesen et al., ). As various alignment methods typically align ambiguous regions differently, phylogenies estimated by the traditional sequential approach can change considerably according to the choice of alignment method (Wong et al., ). (See Web Appendix A for our investigation of the problems of the traditional sequential approach using a simulated data set). A simple approach to avoid these problems is to exclude
Biometrics – Wiley
Published: Jan 1, 2018
Keywords: ; ; ; ; ; ;
It’s your single place to instantly
discover and read the research
that matters to you.
Enjoy affordable access to
over 12 million articles from more than
10,000 peer-reviewed journals.
All for just $49/month
Read as many articles as you need. Full articles with original layout, charts and figures. Read online, from anywhere.
Keep up with your field with Personalized Recommendations and Follow Journals to get automatic updates.
It’s easy to organize your research with our built-in tools.
Read from thousands of the leading scholarly journals from SpringerNature, Elsevier, Wiley-Blackwell, Oxford University Press and more.
All the latest content is available, no embargo periods.
“Hi guys, I cannot tell you how much I love this resource. Incredible. I really believe you've hit the nail on the head with this site in regards to solving the research-purchase issue.”Daniel C.
“Whoa! It’s like Spotify but for academic articles.”@Phil_Robichaud
“I must say, @deepdyve is a fabulous solution to the independent researcher's problem of #access to #information.”@deepthiw
“My last article couldn't be possible without the platform @deepdyve that makes journal papers cheaper.”@JoseServera