The problem with drawing with the JAVA MCscanX

[Wenwen012345]

Hello @BenjaminSchwessinger @jannafierst Recently I have read the literature (https://onlinelibrary.wiley.com/doi/10.1111/jse.12850) and conducted research on LTR- retrotransposon. In this article, the author made the following image using MCscanX. The image seems to be drawn by the Python version of MCscanX, but the method seems to be the old MCscanX method.

Method: "2.6 Syntenic LTR retrotransposons analysis We firstly extracted the coding sequences of all LTR retrotransposons from three chromosome-level genomes, PN40024, V. ripara and V. amurensis genomes. Then the coding sequences were translated into amino acid sequences by using TBtools v1.098 (Chen et al., 2020). Next, multiple sequence alignment inter- and intra-species was performed using blastp of BLAST+ v2.10.1 with ‘-evalue 1e-5,-outfmt 6’ (Camacho et al., 2009), and finally the alignment results were entered into MCScanX (Wang et al., 2012) with default parameters for syntenic analysis. The downstream script ‘duplicate_gene_classifier’ was used to classify origins duplicate LTR retrotransposons into tandem, proximal, dispersed, segmental or singleton. The number of intra-species syntenic LTR retrotransposons and the number of inter-species syntenic LTR retrotransposons was dissected by the script ‘dissect_multiple_alignment’. We clustered the LTR retrotransposons shared among these three genomes according to their syntenic LTR retrotransposons within each genome (results from MCScanX) using Yifan Hu multilevel layout algorithm of Gephi v0.9.2 (https://gephi.org/)."

I used the method used by the authors of this article and got something like this:

What's the matter, please? How can I make figures of MCscanX in Python while using MCscanX in Java?

[Li-Tianran]

That picture seemed to be made by TBtools.

[Wenwen012345]

That picture seemed to be made by TBtools.

Yeah. Thats true. I got a similar graph with TBTOOLS earlier!