Package: wgdi
WGDIAuthorPengchuan Sun (sunpengchuan)Emailsunpengchuan@gmail.comLicenseBSDDescriptionWGDI (Whole-Genome Duplication Integrated analysis), a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidizations and cross-species genome alignments.WGDI supports three main workflows (polyploid inference, hierarchical inference of genomic homology, and ancestral chromosomal karyotyping) that can improve detection of WGD and characterization of related events. It incorporates a more sensitive and accurate collinearity detection algorithm than previous softwares, and can accelerate WGD-related karyotype research.InstallationPython package and command line interface (IDLE) for the analysis of whole genome duplications (WGDI). WGDI can be deployed in Windows, Linux, and Mac OS operating systems and can be installed via pip and conda.Biocondaconda install -c bioconda  wgdiPypipip3 install wgdiDocumentation for installation along with a user tutorial, a default parameter file, and test data are provided. please consult the docs athttp://wgdi.readthedocs.io/en/latest/.TipsHere are some videos with simple examples of WGDI.WGDI的简单使用（一）orhttps://youtu.be/k-S6FVcBIQwWGDI的简单使用（二）orhttps://youtu.be/QiZYFYGclyEchatting group QQ : 966612552Citating WGDIIf you use wgdi in your work, please cite:Sun P., Jiao B., Yang Y., Shan L., Li T., Li X., Xi Z., Wang X., and Liu J. (2022). WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes. Mol. Plant. doi:https://doi.org/10.1016/j.molp.2022.10.018.News0.6.5Fixed some issues (-sf).Added new tips to avoid some errors.0.6.4Fixed the problem caused by the Python version, now it is compatible with version 3.11.3.0.6.3Fixed some issues (-ks, -sf).0.6.2Added find shared fusions between species (-sf).0.6.1Fixed issue with alignment (-a). Only version 0.6.0 has this bug.0.6.0Fixed issue with improved collinearity (-icl).Added a parameter 'tandem_ratio' to blockinfo (-bi).0.5.9Update the improved collinearity (-icl). Faster than before, but lower than MCscanX, JCVI.Fixed issue with ancestral karyotype repertoire (-akr).0.5.8Fixed issue with gene names (-ks).0.5.7Fixed issue with chromosome order (-ak).Fixed issue with gene names (-ks).  This version is not fixed, please install the latest version.0.5.5 and 0.5.6Add ancestral karyotype (-ak)Add ancestral karyotype repertoire (-akr)0.5.4Improved the alignmenttrees (-km) effect.little change (-at).0.5.3Fixed legend issue with (-kf).Fixed calculate Ks issue with (-ks).Improved the karyotype_mapping (-km) effect.Improved the alignmenttrees (-at) effect.0.5.2Fixed some bugs.0.5.1Fixed the error of the command (-conf).Improved the karyotype_mapping (-km) effect.Added the available data set of alignmenttree (-at). Low copy data set (for example, single-copy_groups.tsv of sonicparanoid2 software).0.4.9The latest version adds karyotype_mapping (-km) and karyotype (-k) display.The latest version changes the calculation of extracting pvalue from collinearity (-icl), making this parameter more sensitive. Therefore, it is recommended to set to 0.2 instead of 0.05.The latest version has also changed the drawing display of ksfigure (-kf) to make it more beautiful.