Package: iqtree3
Version: 3.1.1+dfsg-2
Architecture: amd64
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 34102
Depends: libc6 (>= 2.38), libgcc-s1 (>= 4.0), libgomp1 (>= 6), libopenmpi40 (>= 5.0.10), libstdc++6 (>= 14), libyaml-cpp0.8 (>= 0.7.0), zlib1g (>= 1:1.2.6)
Section: science
Priority: optional
Homepage: http://www.iqtree.org
Description: efficient phylogenetic software by maximum likelihood; v3
 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.
 .
 Key features of IQ-TREE
 .
  - Efficient search algorithm: Fast and effective stochastic algorithm
    to reconstruct phylogenetic trees by maximum likelihood. IQ-TREE
    compares favorably to RAxML and PhyML in terms of likelihood while
    requiring similar amount of computing time (Nguyen et al., 2015).
  - Ultrafast bootstrap: An ultrafast bootstrap approximation (UFBoot)
    to assess branch supports. UFBoot is 10 to 40 times faster than
    RAxML rapid bootstrap and obtains less biased support values (Minh
    et al., 2013).
  - Accurate model selection: An ultrafast and automatic model selection
    (ModelFinder) which is 10 to 100 times faster than jModelTest and
    ProtTest. ModelFinder also finds best-fit partitioning scheme like
    PartitionFinder (Kalyaanamoorthy et al., 2017).
  - Alignment simulation: A flexible simulator (AliSim) which allows to
    simulate sequence alignments under more realistic models than
    Seq-Gen and INDELible (Ly-Trong et al., 2023).
  - Phylogenetic testing: Several fast branch tests like SH-aLRT and
    aBayes test (Anisimova et al., 2011) and tree topology tests like
    the approximately unbiased (AU) test (Shimodaira, 2002).
 .
 The strength of IQ-TREE is the availability of a wide variety of
 phylogenetic models:
 .
  - Common models: All common substitution models for DNA, protein,
    codon, binary and morphological data with rate heterogeneity among
    sites and ascertainment bias correction for e.g. SNP data.
  - Partition models: Allowing individual models for different genomic
    loci (e.g. genes or codon positions), mixed data types, mixed rate
    heterogeneity types, linked or unlinked branch lengths between
    partitions.
  - Mixture Models: fully customizable mixture models and empirical
    protein mixture models and.
  - Polymorphism-aware models (PoMo)
    http://www.iqtree.org/doc/Polymorphism-Aware-Models
