jmodeltest.org: selection of nucleotide substitution models on the cloud

Abstract

Summary: The selection of models of nucleotide substitution is one of the major steps of modern phylogenetic analysis. Different tools exist to accomplish this task, among which jModelTest 2 (jMT2) is one of the most popular. Still, to deal with large DNA alignments with hundreds or thousands of loci, users of jMT2 need to have access to High Performance Computing clusters, including installation and configuration capabilities, conditions not always met. Here we present jmodeltest.org, a novel web server for the transparent execution of jMT2 across different platforms and for a wide range of users. Its main benefit is straightforward execution, avoiding any configuration/execution issues, and reducing significantly in most cases the time required to complete the analysis.Availability and implementation: jmodeltest.org is accessible using modern browsers, such as Firefox, Chrome, Opera, Safari and IE from http://jmodeltest.org. User registration is not mandatory, but users wanting to have additional functionalities, like access to previous analyses, have the possibility of opening a user account.Contact: info@jmodeltest.org

Molecular systematics of Abelmoschus (Malvaceae) and genetic diversity within the cultivated species of this genus based on nuclear ITS and chloroplast rpL16 sequence data

“…This program uses a Phi-test of recombination (Bruen et al 2006) to find evidence supporting recombination. An analysis by jModelTest 2 (Darriba et al 2012) showed that models with gamma distribution and invariant sites offered the best fit to the data under both the Akaike and the Bayesian information criteria for the nrITS and the rpL16 regions. MrBayes v3.2 (Ronquist et al 2012) was used for the phylogenetic analyses.…”

Origin and evolution of chloroplast group I introns in lichen algae

“…) as well as with Jmodeltest (Santorum et al. ) for nucleotides and ProtTest3 (Darriba et al. ) for amino acids.…”

Isolation of Tasmanian Rickettsia-like organism (RLO) from farmed salmonids: identification of multiple serotypes and confirmation of pathogenicity

“…The 16S rRNA gene sequences from 2 clones of 10 cultured TRLO isolates (GenBank accession numbers KX691419−KX691438), a cultured New Zealand isolate identified in genome sequence assembly data (NZ-RLO; see BioProject accession number PRJNA 314275; Contig LVCQ01000264) (Gias et al 2016 Santorum et al 2014). For BI, trees were constructed using the K80 substitution model, calculating remaining parameters under the default prior distributions and employing the Monte Carlo Markov chain method (nchains = 4) over 4 000 000 generations, with every 200 th tree being saved.…”

“…The alignment was verified by eye and then subjected to phylogenetic tree searches using Bayesian inference (BI) with MrBayes v.3.2.2 (Huelsenbeck & Ronquist 2001), maximum likelihood (ML) with RAxML v.8.0.24 (Stamatakis 2014) and maximum parsimony (MP) with PAUP* v.4.0 beta (Wilgenbusch & Swofford 2003). For the BI and ML analyses, the K80 nucleotide substitution model (Kimura 1980) was selected using the Bayesian Information Criteria test in jModeltest v.2.1.6 (Santorum et al 2014). For BI, trees were constructed using the K80 substitution model, calculating remaining parameters under the default prior distributions and employing the Monte Carlo Markov chain method (nchains = 4) over 4 000 000 generations, with every 200 th tree being saved.…”

“…Prior to analysis, the oligonucleotide sequences were trimmed from each end of the contigs due to degeneracy in the EubB and EubA primers and the sequences verified using UCHIME version 4.2.40 (Edgar et al 2011). No evidence of chimeric DNA was detected in any of the sequences.The 16S rRNA gene sequences from 2 clones of 10 cultured TRLO isolates (GenBank accession numbers KX691419−KX691438), a cultured New Zealand isolate identified in genome sequence assembly data (NZ-RLO; see BioProject accession number PRJNA 314275; Contig LVCQ01000264) (Gias et al 2016 Santorum et al 2014). For BI, trees were constructed using the K80 substitution model, calculating remaining parameters under the default prior distributions and employing the Monte Carlo Markov chain method (nchains = 4) over 4 000 000 generations, with every 200 th tree being saved.…”