Published in 1994, Yang’s one-parameter model has been used in most of the subsequent molecular phylogenetic research but its success has perhaps also led to his other discovery, in 1995, of a more versatile model (6) of rate heterogeneity across sites being overlooked. ModelFinder includes both models, and the first results show that the more flexible model often is needed to obtain accurate estimates of phylogenetic trees and evolutionary processes.
These results call into question much of the last two decades of phylogenetic research, which relied on phylogenetic methodology that ignored the more versatile model of rate heterogeneity across sites.
The advent of ModelFinder opens a new era of opportunities, where accurate phylogenetic estimates can be obtained and used to answer important biological questions, and where controversial as well as long-standing evolutionary hypotheses can be tested using novel ways of modelling sequence evolution.
ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates
May 8, 2017Publication
This page contains data for the paper:
Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler, and Lars S Jermiin. ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates, Nature Methods. DOI: 10.1038/nmeth.4285.
If no model is specified via -m, IQ-TREE will perform the new model selection, ModelFinder (MF). Accordingly, two new options are introduced: -m MF (equivalent to -m TESTNEWONLY) and -m MFP (equiv. to -m TESTNEW). For backward compatibility TESTNEW will still be available but might be removed in a future release.
Combining standard bootstrap (-b) and constraint tree option (-g) will impose the constraint on bootstrap trees (previously not). Thanks to Matthew Prebus for discussions.
The precompiled Linux executables are now backward compatible with the old Linux kernel 2.X, which resolves the error message “FATAL: kernel too old”.
Support input files with different newline formats to resolve conflicts between Mac, Windows or Linux files.
For data sets with identical sequences, redundant sequences are ignored. However, IQ-TREE will now keep two identical sequences (i.e. if five sequences A,B,C,D,E are identical to each other, then A,B are kept and C,D,E are ignored). This avoids incompatibility between bootstrap and non-bootstrap runs.
Warning about too many threads for short alignments (reported by Joran Martijn).
New option -wbsf to print individual bootstrap alignments and sitefreq files for standard bootstrap (requested by Huaichun Wang).
Segfault caused by combining standard bootstrap, partition model and constraint tree (reported by Matthew Prebus).
Crash by -nni1 option (reported by Carlos Rivera).
Illegal instruction on older Mac which does not support AVX instruction set (reported by Richard Moir and Matthew Fullmer).
Crash when combining -mtree and -bb during model selection (reported by Chris Buddenhagen).
We are pleased to announce version 1.5.1 with special focus on huge data sets and supercomputing with following new features:
Merged the parallel MPI version with much better parallel efficiency and scalability. The old MPI version is deprecated.
Memory saving mode via a new -mem option to restrict RAM usage, helpful for complex mixture models. For example, -mem 64G to use at most 64 GB. By default, IQ-TREE will try to fit the computer RAM size. Note that this mode does not work with partition models yet.
Safe numerical mode for huge data sets to avoid “Numerical underflow” errors. This mode is automatically turned on when having more than 2000 sequences. It can be manually turned on via -safe option.
New option -nt AUTO to automatically determine best number of threads in multicore version.
We are pleased to announce IQ-TREE version 1.5.0 with following major updates:
Major new features:
A new posterior mean site frequency (PMSF) model as a rapid approximation to the time and memory consuming CAT profile mixture models C10 to C60 (Le et al., 2008a). The PMSF model is much faster and requires much less RAM than the mixture models, regardless of the number of mixture classes. This allows, for the first time, to conduct nonparametric bootstrap under such complex models. Our extensive simulations and empirical deep-phylogeny data analyses demonstrate that the PMSF models can effectively ameliorate long branch attraction artefacts. For details see http://www.iqtree.org/doc/Complex-Models#site-specific-frequency-models
New option -g to supply a user-defined constraint tree, which will guide subsequent tree search. The constraint tree can be multifurcating and need not to include all taxa.
Crash with zero weights of mixture models for short alignments (thanks to Laura Eme for the report).
Incorrect site rate file (-wsr option) in the presence of identical sequences (thanks to Brian Foley for the report).
Memory overflow for tree topology testing for extremely long alignments (>500,000 sites) (thanks to Karen Meusemann for the report).
Rare issue with multifurcating trees and partition model (thanks to Xingxing for the report).
A new biologist-familiar example data file example.phy, which contains mitochondrial DNAs of human, gorilla, dog, mouse, etc. The data set was taken from the phylogenetic handbook (thanks to Brian Foley for suggestion).
Printing an alignment with suffix .varsite with only variable sites if ascertainment bias correction (ASC) is not applicable.
New option -wpl to write partition-specific log-likelihoods to .partlh file (requested by Karen Meusemann).