.. wgd documentation master file, created by sphinx-quickstart on Mon Apr 10 10:31:22 2017. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. wgd: Whole genome duplication analysis in Python ************************************************ This Python package and corresponding command line interface (CLI) were developed for various analyses related to whole genome duplications (WGDs). Here the Python API is documented as well as the various command line utilities bundled in the ``wgd`` CLI. Installation ============ To install ``wgd``, go to the repository available at https://github.com/arzwa/wgd and follow installation instructions there. Example & information ===================== - To **get started** with ``wgd`` head straight to the :ref:`command line interface page `. - For more **information** on |Ks| distributions and how ``wgd`` computes them have a look at :ref:`these notes. ` - For an additional **step by step example**, we refer to the supplementary information of our Bioinformatics Applications note paper (open access) at https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty915/5162749 External software ================= ``wgd`` requires the following third party executables (preferably these should also be in the ``PATH`` environment variable): For ``wgd blast``: - BLAST, from which it uses the ``blastp`` and ``makeblastdb`` commands, ``sudo apt-get install ncbi-blast+`` will often suffice for installation - MCL (https://micans.org/mcl/index.html). Get MCL using your package manager ``sudo apt-get install mcl`` or download it at the provided link. For ``wgd ks`` (most of these can also be installed with ``apt-get``): - One of the following multiple sequence alignment programs: MUSCLE, MAFFT or PRANK (``sudo apt-get install muscle mafft prank``) - CODEML from the PAML software package (Yang 1997). PAML can be downloaded from the following link: http://abacus.gene.ucl.ac.uk/software/paml.html. It can also be installed using ``sudo apt-get install paml``. - For node weighting using phylogenetic trees, PhyML and FastTree are supported, but average linkage clustering (no external software needed) can be used as an alternative. To install ``sudo apt-get install fasttree phyml``. (Note that FastTree should be executable as ``FastTree`` and not ``fasttree``, so please specify an alias or symlink from the latter to the former if necessary.) For ``wgd syn`` - i-ADHoRe 3.0 suite (http://bioinformatics.psb.ugent.be/beg/tools/i-adhore30) Of course, you don't need all of these tools installed for each feature of ``wgd``. Command line tools ================== The command line tools are the main functionality of the ``wgd`` package. You can find tools for the following analyses: 1. All-*versus*-all Blastp analysis and MCL clustering 2. Whole paranome |Ks| (and |Ka| and ω) distribution construction 3. One-versus-one orthologs |Ks| (and |Ka| and ω;) distribution construction 4. Mixture modeling of |Ks| distributions and WGD-specific paralog extraction 5. Interactive visualization of (multiple) |Ks| distributions and kernel density estimates thereof 6. Intragenomic co-linearity/synteny analysis and anchor based |Ks| distribution construction 7. Co-linearity dotplot construction All information can be found here: .. toctree:: :maxdepth: 1 Command line interface Here is a flow chart of the different analyses that can be performed using the wgd CLI: .. image:: flowchart.png Citation ======== If you use ``wgd``, please cite:: - Zwaenepoel, A., and Van de Peer, Y. wgd - simple command line tools for the analysis of ancient whole genome duplications. Bioinformatics., bty915, https://doi.org/10.1093/bioinformatics/bty915 Furthermore, for the specific tools in ``wgd``, please cite the following: If you use ``wgd mcl`` please cite:: - Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389–3402. - van Dongen, S. (2000). Graph Clustering by Flow Simulation. Ph.D. thesis, University of Utrecht, Utrecht. For ``wgd ksd``, please cite:: - Yang, Z. (2007). PAML 4: Phylogenetic Analysis by Maximum Likelihood. Molecular Biology and Evolution, 24(8), 1586–1591. - [if using MUSCLE] Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792–1797. - [if using MAFFT] Katoh, K. and Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution, 30(4), 772–780. - [if using PRANK] Löytynoja, A. and Goldman, N. (2008). Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis. Science, 320(5883), 1632–1635. - [if using FastTree] 2825–2830. Price, M. N., Dehal, P. S., and Arkin, A. P. (2010). FastTree 2 - Approximately Maximum-Likelihood Trees for Large Alignments. PLOS ONE, 5(3), e9490. - [if using PhyML] Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., and Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology, 59(3), 307–321. For ``wgd syn``, please cite:: - Proost, S., Fostier, J., De Witte, D., Dhoedt, B., Demeester, P., Van de Peer, Y., and Vandepoele, K. (2012). i-ADHoRe 3.0 : fast and sensitive detection of genomic homology in extremely large data sets. NUCLEIC ACIDS RESEARCH, 40(2). Python package ============== For those interested in the underlying structure of ``wgd``, here you can find the full documentation of the API. Contents: .. toctree:: :maxdepth: 2 Blast & Markov clustering (MCL) Codeml anlysis Alignment tools Ks distribution analysis Phylogenetics tools Mixture modeling Co-linearity analysis Utilities Visualization Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search` .. |Ks| replace:: K\ :sub:`S` .. |Ka| replace:: K\ :sub:`A`