Visualized comparative genomic methods

比较基因组学工具，用来可视化多基因组（跨物种/不同个体）比对信息，或者是基因的共线性信息。

Reading materials

• Whole-Genome Alignment

• 聊聊基因组共线性

• geneCo: a visualized comparative genomic method to analyze multiple genome structures
  web: https://bigdata.dongguk.edu/geneCo
  paper: https://academic.oup.com/bioinformatics/article/35/24/5303/5539862

• M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species

download: http://alggen.lsi.upc.es/recerca/align/mgcat/intro-mgcat.html
paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-433

• FlexiDot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses
  github: https://github.com/molbio-dresden/flexidot
  paper: https://academic.oup.com/bioinformatics/article/34/20/3575/4995848

• GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface
  github: https://github.com/JulienLajugie/GenPlay
  paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4402384/

• Ensembl, Compare genes across species
  https://asia.ensembl.org/info/website/tutorials/compara.html

• Combining Strengths for Multi-genome Visual Analytics Comparison
  github: https://github.com/Bitlab-UMA
  paper: https://journals.sagepub.com/doi/10.1177/1177932218825127

• gggenes,
  github: https://github.com/wilkox/gggenes
  examples: https://cloud.tencent.com/developer/article/1534338

• Mummer4,
  mummerplot

• Genomicus
  Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.
  web: https://www.genomicus.biologie.ens.fr/genomicus-metazoa-30.01/cgi-bin/search.pl

• Circos

• R package: RIdeogram

• TBtools
  examples: https://www.jianshu.com/p/45bece9a0518
  https://www.jianshu.com/p/2334a6346941

• mauve
  适合小基因组的比对分析， 例如线粒体，叶绿体，质粒的基因组，还有细菌，病毒的基因组。
  web: http://darlinglab.org/mauve/mauve.html
  example: https://zhuanlan.zhihu.com/p/359203720

• Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements
  github: https://github.com/smortezah/smashpp
  paper: https://academic.oup.com/gigascience/article/9/5/giaa048/5841055