IQ-TREE - Efficient phylogenomic software by maximum likelihood

  •        170

The IQ-TREE software was created as the successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the rapid accumulation of phylogenomic data, leading to a need for efficient phylogenomic software that can handle a large amount of data and provide more complex models of sequence evolution. To this end, IQ-TREE can utilize multicore computers and distributed parallel computing to speed up the analysis. IQ-TREE automatically performs checkpointing to resume an interrupted analysis. As input IQ-TREE accepts all common sequence alignment formats including PHYLIP, FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a self-readable report file (name suffix .iqtree), a NEWICK tree file (.treefile) which can be visualized by tree viewer programs such as FigTree, Dendroscope or iTOL.



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NEX_WRITE_TEMPLATE_RAM (426) writes arbitrary data into Template RAM that stores the raw IQ samples that we may transmit. The ioctl's payload contains (1) an int32 value indicating the offset where data should be written in Template RAM in bytes, (2) an int32 value indicating the length of the data that should be written and (3) the IQ samples as array of IQ values, where I (inphase components) and Q (quadrature components) are stored as int16 numbers. NEX_SDR_START_TRANSMISSION (427) that triggers the transmission of IQ samples. The ioctl's payload contains (1) an int32 value indicating the number of samples to transmit, (2) an int32 value indicating the offset where the signal starts in Template RAM, (3) an int32 value indicating a chanspec (channel number, bandwidth, band, ...), (4) an int32 value indicating the power index (lower value means higher output power), and (5) an int32 value indicating whether to loop over the IQ samples or transmit them only once.

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