![]() ![]() ModelFinder implements a greedy strategy ( Lanfear et al., 2012) that starts with the full partition model and subsequentially merges two genes until the model fit does not increase any further: iqtree -s example.phy -p example.nex -m MFP+MERGE For your convenience IQ-TREE writes the concatenated alignment into the file. For instance, if some sequence occurs in aln.phy but not in prot.phy, IQ-TREE will treat the corresponding parts of sequence in prot.phy as missing data. Note that aln.phy and prot.phy does not need to contain the same set of sequences. If you want to use another genetic code, append CODON with the code ID described hereīecause the alignment file names are now specified in this NEXUS file, you can omit the -s option: iqtree -p example.nex Moreover, this implicitly assumes the standard genetic code. TIP: For part5 the CODON keyword is specified so that IQ-TREE will apply a codon model. ![]() Note that, for convenience * in part5 specification means that part5 corresponds to the entire alignment codon.phy. The : is needed to separate the alignment file name and site specification. Here, part1 and part2 contain sub-alignments from alignment file dna.phy, whereas part3 and part4 are loaded from alignment file prot.phy and part5 from codon.phy. Here is an example for mixing DNA, protein and codon models: #nexusĬharpartition mine = HKY:part1, GTR+G:part2, LG+G:part3, WAG+I+G:part4, GY:part5 IQ-TREE also allows combining sub-alignments from different alignment files, which is helpful if you want to combine mixed data (e.g. This is useful for getting codon positions from the protein-coding alignment. Another example is: charset part1 = 1-100\3 įor extracting sites 1,4,7,…,100 from the alignment. That means, part1 contains sites 1-100 and 200-384 of the alignment. Moreover, the CharSet command allows to specify non-consecutive sites with e.g.: charset part1 = 1-100 200-384 Substitution model parameters and trees with branch lengths can be found in the result file. Moreover, IQ-TREE applies the subtitution models HKY+G and GTR+I+G to part1 and part2, respectively. Here, IQ-TREE partitions the alignment example.phy into 2 sub-alignments named part1 and part2 containing sites (columns) 1-100 and 101-384, respectively. If your NEXUS file is called example.nex, then you can use the option -p to input the file as following: iqtree -s example.phy -p example.nex For example: #nexusĬharpartition mine = HKY+G:part1, GTR+I+G:part2 This file contains a SETS block with CharSet and CharPartition commands to specify individual genes and the partition, respectively. If you want to specify, say, +G for the first partition and +I+G for the second partition, then you need to create the more flexible NEXUS partition file. Note that using RAxML-style partition file, all partitions will use the same rate heterogeneity model given in -m option ( +I+G in this example). If your partition file is called example.partitions, the partition analysis can be run with: iqtree -s example.phy -p example.partitions -m GTR+I+G The RAxML-style partition file may look like: DNA, part1 = 1-100 IQ-TREE supports RAxML-style and NEXUS partition input file. the BIC scores to determine the best-fit partition model. One can also perform all three analyses and compare e.g. q is unrealistic and -Q is very parameter-rich. NOTE: -p is recommended for typical analysis. -Q partition_file ( -sp in version 1.x): each partition has its own set of branch lengths (like combination of -q and -M options in RAxML) to account for, e.g.-p partition_file ( -spp in version 1.x): like above but allowing each partition to have its own evolution rate.-q partition_file: all partitions share the same set of branch lengths (like -q option of RAxML).Moreover, IQ-TREE provides edge-linked or edge-unlinked branch lengths between partitions: IQ-TREE will then estimate the model parameters separately for every partition. In the partition model, you can specify a substitution model for each gene/character set. Minh (2016) Terrace aware data structure for phylogenomic inference from supermatrices. If you used partition model in a publication please cite: ![]()
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