PMID- 27103098
OWN - NLM
STAT- MEDLINE
DCOM- 20171211
LR  - 20200306
IS  - 1477-4054 (Electronic)
IS  - 1467-5463 (Print)
IS  - 1467-5463 (Linking)
VI  - 18
IP  - 3
DP  - 2017 May 1
TI  - Heterogeneous molecular processes among the causes of how sequence similarity 
      scores can fail to recapitulate phylogeny.
PG  - 451-457
LID - 10.1093/bib/bbw034 [doi]
AB  - Sequence similarity tools like Basic Local Alignment Search Tool (BLAST) are 
      essential components of many functional genetic, genomic, phylogenetic and 
      bioinformatic studies. Many modern analysis pipelines use significant sequence 
      similarity scores (p- or E-values) and the ranked order of BLAST matches to test 
      a wide range of hypotheses concerning homology, orthology, the timing of de novo 
      gene birth/death and gene family expansion/contraction. Despite significant 
      contrary findings, many of these tests still implicitly assume that stronger or 
      higher-ranked E-value scores imply closer phylogenetic relationships between 
      sequences. Here, we demonstrate that even though a general relationship does 
      exist between the phylogenetic distance of two sequences and their E-value, 
      significant and misleading errors occur in both the completeness and the order of 
      results under realistic evolutionary scenarios. These results provide additional 
      details to past evidence showing that studies should avoid drawing direct 
      inferences of evolutionary relatedness from measures of sequence similarity 
      alone, and should instead, where possible, use more rigorous phylogeny-based 
      methods.
CI  - (c) The Author 2016. Published by Oxford University Press.
FAU - Smith, Stephen A
AU  - Smith SA
FAU - Pease, James B
AU  - Pease JB
LA  - eng
PT  - Journal Article
PL  - England
TA  - Brief Bioinform
JT  - Briefings in bioinformatics
JID - 100912837
SB  - IM
MH  - Computational Biology
MH  - *Phylogeny
MH  - Sequence Alignment
MH  - Software
PMC - PMC5429007
OTO - NOTNLM
OT  - BLAST
OT  - compositional bias
OT  - phylogenetics
OT  - phylostratigraphy
OT  - rate heterogeneity
OT  - sequence similarity
EDAT- 2016/04/23 06:00
MHDA- 2017/12/12 06:00
PMCR- 2016/04/21
CRDT- 2016/04/23 06:00
PHST- 2016/01/19 00:00 [received]
PHST- 2016/04/23 06:00 [pubmed]
PHST- 2017/12/12 06:00 [medline]
PHST- 2016/04/23 06:00 [entrez]
PHST- 2016/04/21 00:00 [pmc-release]
AID - bbw034 [pii]
AID - 10.1093/bib/bbw034 [doi]
PST - ppublish
SO  - Brief Bioinform. 2017 May 1;18(3):451-457. doi: 10.1093/bib/bbw034.