m is the option to specify the model name to use during the analysis. # change -m MFP to -m TEST to resemble jModelTest/ProtTest If you do not know which model is appropriate for your data, you can use ModelFinder to determine the best-fit model: iqtree -s example.phy -m MFP IQ-TREE supports a wide range of substitution models for DNA, protein, codon, binary and morphological alignments. Jermiin (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. NOTE: If you use model selection please cite the following paper: This prevents output files being overwritten when you perform multiple analyses on the same alignment within the same folder. You canĬhange the prefix with: iqtree -s example.phy -prefix myprefix However, if you really want to re-run the analysis and overwrite all previous output files, use -redo option: iqtree -s example.phy -redoįinally, the default prefix of all output files is the alignment file name. This prevents lost of data if you accidentally re-run IQ-TREE. Use `-redo` option if you really want to redo the analysis and overwrite all output files. If the run successfully completed, running again will issue an error message: ERROR: Checkpoint () indicates that a previous run successfully finished If the run did not finish, invoking IQ-TREE again with the very same command line will recover the analysis from the last stopped point, thus saving all computation time done before. This checkpoint file is used to resume an interrupted run, which is handy if you have a very large data sets or time limit on a cluster system. However, please note that IQ-TREE always produces an unrooted tree as it knows nothing about this biological background IQ-TREE simply draws the tree this way as LngfishAu is the first sequence occuring in the alignment.ĭuring the example run above, IQ-TREE periodically wrote to disk a checkpoint file (gzip-compressed to save space). Here the tree is drawn at the outgroup Lungfish which is more accient than other species in this example. This makes sense as the mammals ( Human to Opossum) form a clade, whereas the reptiles ( Turtle to Crocodile) and Bird form a separate sister clade. iqtree file): NOTE: Tree is UNROOTED although outgroup taxon 'LngfishAu' is drawn at root To report bugs, please send this log file and the original alignment file to the authors.įor this example data the resulting maximum-likelihood tree may look like this (extracted from. : log file of the entire run (also printed on the screen).: the ML tree in NEWICK format, which can be visualized by any supported tree viewer programs like FigTree or iTOL.It also contains a textual representation of the final tree (see below). You should look at this file to see the computational results. : the main report file that is self-readable.At the end of the run IQ-TREE will write several output files including: s is the option to specify the name of the alignment file that is always required by IQ-TREE to work. You can now start to reconstruct a maximum-likelihood tree from this alignment by entering (assuming that you are now in the same folder with example.phy): iqtree -s example.phy This example contains parts of the mitochondrial DNA sequences of several animals (Source: Phylogenetic Handbook).
How to convert a file to fasta format in mega 7 download#
First running exampleįrom the download there is an example alignment called example.phy in PHYLIP format. IQ-TREE 2 will load and concatenate all alignments within the directory, eliminating the need for users to manually perform this step. TIP: From version 2 you can input a directory of alignment files. The FASTA file for the above example may look like this: >Frog IQ-TREE also supports other file formats such as FASTA, NEXUS, CLUSTALW. This tiny alignment contains 7 DNA sequences from several animals with the sequence length of 28 nucleotides. For example the PHYLIP format which may look like: 7 28 The input alignment can be in various common formats. If you have raw (unaligned) sequences, you need to first run an alignment program like MAFFT or ClustalW to align the sequences, before feeding them into IQ-TREE. IQ-TREE takes as input a multiple sequence alignment and will reconstruct an evolutionary tree that is best explained by the input data.