Polyploidy and subsequent gene loss and diploidization are present in most species and are important drivers of species evolution. If a species has undergone polyploidization during evolution, then there will be some covariant regions (i.e., the genes between two regions are paralogous homologous genes, and the order of their genes is basically the same) on…

I: Download and install The latest version of the Pfam database no longer has Pfam-B, so you can download Pfam-A.hmm, Pfam-A.hmm.dat and active_site.dat directly, and then unzip the downloaded files: gunzip Pfam-A.hmm.gz Pfam-A.hmm.dat.gz active_site .dat.gz II: Formatting the Pfam database via hmmerspress III: Running the program IV: Format of results The results of pfamscan protein…

If you want to use JBrowse, you must have administrator rights, otherwise IGV is recommended. Pre-requirements Your server must have libpng,zlib,libgd,make,C compiler, C++ compiler installed. There are different installation methods for different operating systems. If you have administrator privileges, you can just use the system’s own management tools. Note: If you don’t have administrator privileges,…

RepeatMasker is a specialized software for genome repetitive sequence identification annotation, and classification statistics for almost all species. It is essential software for studying genomes, non-coding RNAs, transposons and mitotic collaterals and other related fields. Many small RNAs, lncRNAs are closely related to Repeat regions. Software Installation and Configuration The installation environment for Ubuntu 16.04.2…

HMMER is a bioinformatics software used to analyze gene sequences to quickly determine the degree of similarity between two sets of sequences, and the latest version is 3.1. However, the official website of HMMER only provides the Linux version, and the Windows version is inactive. Maybe the sequence analysis software can only work well on…