Why IQ-TREE? Bui Quang Minh Australian National University. Workshop on Molecular Evolution Woods Hole, 24 July 2018

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1 Why IQ-R? ui Quang Minh ustralian National University Workshop on Molecular volution Woods Hole, 24 July 2018

2 hanks to plenty of users for feedback and bug reports!

3 ypical phylogenetic analysis under maximum likelihood Multiple sequence alignment Model selection Substitution model hallenges - lood of sequence data - Need for realistic models of sequence evolution ree reconstruction % 94% ranch supports -- 63% ree with branch supports Phylogenetic tree

4 ypical phylogenetic analysis under maximum likelihood Multiple sequence alignment Substitution model Model selection Modelinder -- 85% % 94% Ultrafast bootstrap ranch supports -- IQ-R ree reconstruction ree with branch supports Phylogenetic tree

5 dvanced models of sequence evolution Substitution models N Protein odon inary and Morphological Partition models dge-linked (equal or proportional) dge-unlinked Polymorphism-aware models (PoMo) ombining phylogenetic (mutations) with population genetics (drift) models. Rate heterogeneity across sites Invariant sites amma model reerate model (available PhyML, RxML- N, IQ-R, PML, S2, Revayes) Mixture models Mixture of rate matrices (L4M, L4X) Mixture of state frequencies (10-60) Mixed branch lengths (HOS eneral Heterotachy on Single rees) User-defined mixtures Site-specific models Posterior mean site frequency (PMS) ll models automatically selected with Modelinder. lot faster than jmodelest and Protest!

6 ree reconstruction: Which tree best explains the data? itations per year Year Source: phylobotanist.blogspot.com

7 IQ-R: new tree search algorithm L.. Nguyen, H. Schmidt,. von Haeseler Maximum parsimony Nearest neighbor interchange (NNI) Random NNIs

8 enchmark: Log-likelihood maximisation etter 0 Log likelihood differences from max Worse M.NNI M.SPR5 astree PhyML RxML RLI IQR Independently confirmed by Zhou, Rokas et al. (2018)

9 Runtimes Slow ast

10 ranch supports: How reliable are branches of the tree?..u.. lignment..uu uuu.. ML tree Sample 1 Sample 2..U....U UUUU....UUUU....UUUU UUU.. ree 1 ree onsensus tree Sample x..uu....uu u.. ree x ootstrap analysis is extremely time-consuming!

Uoot: Ultrafast bootstrap approximation lignment Resampling stimated site Log Likelihoods (RLL) 107 236 124 143 175 134 305 281 117 262 151 144 127 317 250 321 131 258 125

117 127 117 317 262 317 250 250 117 151 140 200 286 131 139 258 139 258 286 258 286 125 286 140 131 139 131 200 258 200 286 286 131 125 ML tree search with the IQ R

ree 2 RLL sample 1 for tree 2 RLL sample 2 for tree 2 RLL sample y for tree 2 ree x estimated site log likelihoods from the original alignment RLL sample 1 for tree x RLL

11 Uoot: Ultrafast bootstrap approximation lignment Resampling stimated site Log Likelihoods (RLL) ML tree search with the IQ R strategy ree 1 many trees collected during tree search with their estimated site log likelihoods RLL sample 1 for tree 1 RLL sample 2 for tree 1 RLL sample y for tree 1 ree 2 RLL sample 1 for tree 2 RLL sample 2 for tree 2 RLL sample y for tree 2 ree x estimated site log likelihoods from the original alignment RLL sample 1 for tree x RLL sample 2 for tree x RLL sample y for tree x ML tree best RLL trees ree ree ree y M... Nguyen,. von Haeseler ML tree with Uoot proportions map branch proportions onto ML tree

12 Other features ootstrap resampling Resampling partitions Resampling partitions and sites Single branch tests SH-aLR (Shimodaira-Hasegaw-like approximate likelihood ratio test) aayes ree topology tests Shimodaira-Haegawa (SH) test xpected Likelihood Weight (LW) Post-analysis ncestral sequence reconstruction Inferring site-specific rates IQ-R forum: for questions, complaints, etc.

13 xercises Single model on a N data set (obtained from Phylogenetic Handbook) irst running example hoosing the right substitution model ssessing branch supports (Uoot, SH-aLR) Utilizing multi-core PUs Partition model on a 248-gene urtle N data set (kindly provided by J. rown) Partitioned analysis for multi-gene alignments hoosing the right partitioning scheme (*optional) ootstrap resampling partitions ree tests Identifying most influential genes (*optional) Mixture model on a 10-gene Microsporidia protein data set (kindly provided by L. me) Protein mixture model analysis

Phylogenetics. Applications of phylogenetics. Unrooted networks vs. rooted trees. Outline

Phylogenetics. Applications of phylogenetics. Unrooted networks vs. rooted trees. Outline Phylogenetics Todd Vision iology 522 March 26, 2007 pplications of phylogenetics Studying organismal or biogeographic history Systematics ating events in the fossil record onservation biology Studying