![]() Note: for chr#, a two-letter short name is used as prefix for the species # is the chromosome number. The xyz.bed file holds gene positions, following a tab-delimited format: chr# starting_position ending_position gene Here is a typical parameter setting for generating the xyz.blast file: $blastall -i query_file -d database -p blastp -e 1e-10 -b 5 -v 5 -m 8 -o xyz.blast The xyz.blast file is simply the direct BLASTP output of m8 format as following: AT1G50920 AT1G50920 100.00 671 0 0 1 671 1 671 0.0 1316 MCscan2 reads in two data files: xyz.blast and xyz.gff. This program, implementing a modified MCScan algorithm, detects syntenic blocks and progressively aligns multiple syntenic blocks against reference genomes (PIVOT). The following is the list of executable programsĭownstream analysis programs (in the downstream_analyses folder) Simply put MCscanX.zip into a directory and run: $unzip MCscanx.zip To show them on the screen, users just need to run the program without giving any options: $./program_nameĪll code is copiable, distributable, modifiable, and usable without any restrictions.Ĭontact: Yupeng Wang, Xu Tan, Installation Make Usage or help information are well built into the programs. The MCScanX package has two major components: a modified version of MCscan algorithm allowing users to handle MCScan more conveniently and to view multiple alignment of syntenic blocks more clearly, and a variety of downstream analysis tools to conduct different biological analyses based on the synteny data generated by the modified MCScan algorithm.Īll programs are executed using command line options on Linux systems or Mac OS. The following is the list of executable programs.
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