VNU-UET Repository: No conditions. Results ordered -Date Deposited. 2024-03-28T18:15:08ZEPrintshttp://eprints.uet.vnu.edu.vn/images/sitelogo.pnghttps://eprints.uet.vnu.edu.vn/eprints/2018-06-01T03:49:04Z2018-06-01T03:49:04Zhttp://eprints.uet.vnu.edu.vn/eprints/id/eprint/2955This item is in the repository with the URL: http://eprints.uet.vnu.edu.vn/eprints/id/eprint/29552018-06-01T03:49:04ZMPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximationBACKGROUND:
The nonparametric bootstrap is widely used to measure the branch support of phylogenetic trees. However, bootstrapping is computationally expensive and remains a bottleneck in phylogenetic analyses. Recently, an ultrafast bootstrap approximation (UFBoot) approach was proposed for maximum likelihood analyses. However, such an approach is still missing for maximum parsimony.
RESULTS:
To close this gap we present MPBoot, an adaptation and extension of UFBoot to compute branch supports under the maximum parsimony principle. MPBoot works for both uniform and non-uniform cost matrices. Our analyses on biological DNA and protein showed that under uniform cost matrices, MPBoot runs on average 4.7 (DNA) to 7 times (protein data) (range: 1.2-20.7) faster than the standard parsimony bootstrap implemented in PAUP*; but 1.6 (DNA) to 4.1 times (protein data) slower than the standard bootstrap with a fast search routine in TNT (fast-TNT). However, for non-uniform cost matrices MPBoot is 5 (DNA) to 13 times (protein data) (range:0.3-63.9) faster than fast-TNT. We note that MPBoot achieves better scores more frequently than PAUP* and fast-TNT. However, this effect is less pronounced if an intensive but slower search in TNT is invoked. Moreover, experiments on large-scale simulated data show that while both PAUP* and TNT bootstrap estimates are too conservative, MPBoot bootstrap estimates appear more unbiased.
CONCLUSIONS:
MPBoot provides an efficient alternative to the standard maximum parsimony bootstrap procedure. It shows favorable performance in terms of run time, the capability of finding a maximum parsimony tree, and high bootstrap accuracy on simulated as well as empirical data sets. MPBoot is easy-to-use, open-source and available at http://www.cibiv.at/software/mpboot .Thi Diep Hoangdiepht@vnu.edu.vnSy Vinh Levinhls@vnu.edu.vnTomas FlouriAlexandros StamatakisArndt von HaeselerQuang Minh Bui2016-12-29T08:23:45Z2017-01-06T07:14:56Zhttp://eprints.uet.vnu.edu.vn/eprints/id/eprint/2358This item is in the repository with the URL: http://eprints.uet.vnu.edu.vn/eprints/id/eprint/23582016-12-29T08:23:45ZUltrafast Parsimony BootstrapThi Diep Hoangdiepht@vnu.edu.vnArndt von HaeselerQuang Minh Bui2016-12-29T08:22:47Z2016-12-29T08:22:47Zhttp://eprints.uet.vnu.edu.vn/eprints/id/eprint/2355This item is in the repository with the URL: http://eprints.uet.vnu.edu.vn/eprints/id/eprint/23552016-12-29T08:22:47ZA new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementationReconstructing maximum parsimony (MP) trees along with bootstrap for large multiple sequence alignments is a computationally challenging task. In this paper, we present MPBoot, a new method for approximating MP bootstrap based on the idea of a previously introduced method for maximum likelihood bootstrap. MPBoot economizes the computations by only sampling trees on the original alignment and simultaneously calculating exact parsimony scores for all bootstrap alignments. Preliminary experiments on simulated data showed that MPBoot is about 2-3.5 times faster and yields better parsimony scores than a fast bootstrap procedure implemented in TNT. MPBoot also produced less biased support value than TNT for small simulated data sets (<;= 200 sequences). However, for large number of sequences (>=500) MPBoot overestimates the probability that a clade is true, i.e., results in likely high false positive rates. As MPBoot is currently a proof-of-concept implementation, more work is to understand the limitations of the method.Thi Diep Hoangdiepht@vnu.edu.vnLe Sy VinhTomas FlouriAlexandros StamatakisArndt von HaeselerBui Quang Minh