Effortless phylogenetic tree building using your choice of algorithm Choose the Neighbor Joining (BIONJ) phylogenetic tree building method or choose any of three methods based on Maximum Likelihood (RAxML, RAxML-NG, IQ-Tree). Customize phylogenetic tree generator parameters, if desired. Use bootstrap ...
Overall information of the bladder microbiota culture collection.A–DDistribution of genome assembly, completeness, contamination, coverage (on a log10 scale), and L50 values, respectively.EPhylogenomic tree of the 196 bacterial species (assigned by GTDB) represented in the bladder genome collection. ...
assemblies and genomes (Figs.4,S2). While the overall topology of the tree grossly agrees with previously published phylogenies derived from concatenated housekeeping genes47,48, several novel observations can be made. Similar to the ribosomal protein tree49...
From these 1000 trees, we calculated a maximum clade credibility tree using mean node heights with the software TreeAnnotator of the BEAST 2 package for use in subsequent analyses46. Functional traits and phylogenetic structure of waterbird communities Four functional traits were selected to calculate ...
--ehcpCheck input organisms prepare for extend autobuild tree module. --srnaCheck whether organisms are supported in the SILVA database. Frequently Asked Questions (FAQ) 1.What is the input of PhySpeTree? Users only need to prepare a TXT file containingKEGGabbreviated species names. For example...
1976). Specifically, the first assigned branch after the common eukaryotic ancestor from NCBI’s Common Tree was used as the blocking variable, and the feature of interest was used as the group variable. If a particular feature was only found to take different values in a single clade, the ...
(1) to report the first complete cp genome of the genusPolystachyaand to reveal the structure and sequence variation of plastomes withinPolystachya, (2) to reconstruct a more comprehensive and better-resolved phylogenetic tree for exploring the phylogenetic position ofPolystachyain Orchidaceae and (3)...
The tree prior was specified as a Yule process. Tracer v.1.5 [81] was used to assess chain convergence and to ensure that the effective sample sizes (ESS) were greater than 200. The maximum clade credibility (MCC) tree with median heights was computed using TreeAnnotator v2.6.6. Four ...
A maximum credibility tree was generated with TREEANNOTATOR v.1.8.176 discarding 25% of the trees as a burn-in after checking the ESS values and a plateau phase in TRACER v.1.681. Further, we used the database of biogeographic distribution data11 to relate the phylogenetic diversity (estimated...
Jobb G: TREEFINDER. Version of October 2008. Munich, Germany. Distributed by the author at http://www.treefinder.de Shimodaira H, Hasegawa M: Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol. 1999, 16: 1114-1116. Article CAS Google Scholar ...