Comments (2)
Hi @Yuki0902,
The --mo
parameter gives you the similarity scores between the input clusters (i.e. calculated from all gene alignments between two clusters). This is the matrix that is used in the clustering step which determines the display ordering of the clusters in the output. The names are taken from the input cluster files. For instance, running clinker on the files in the examples
folder gives the following:
,A. alliaceus CBS 536.65,A. burnettii MST-FP2249,A. mulundensis DSM 5745,A. versicolor CBS 583.65,P. vexata CBS 129021
A. alliaceus CBS 536.65,0.0,0.0,0.22350406073456497,0.3042042558254481,0.6034166451441612
A. burnettii MST-FP2249,0.0,0.0,0.23137351943160522,0.3408531051603084,0.6204295216720592
A. mulundensis DSM 5745,0.22350406073456497,0.23137351943160522,0.0,0.35355579358610445,0.6219765052472899
A. versicolor CBS 583.65,0.3042042558254481,0.3408531051603084,0.35355579358610445,0.0,0.6141102008013652
P. vexata CBS 129021,0.6034166451441612,0.6204295216720592,0.6219765052472899,0.6141102008013652,0.0
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Thank you for your response, which has provided me with more insights into this parameter :)!. However, I still have some doubts regarding the calculations with the --mo parameter. After running the calculations on the gbk files in the 'examples' folder, I noticed that the similarity between A. burnettii MST-FP2249 and A. alliaceus CBS 536.65 appears to be zero when using the --mo parameter. On the other hand, the results with the --p parameter indicate that the similarity between A. burnettii MST-FP2249 and A. alliaceus CBS 536.65 for different functional genes is mostly above 0.7. I'm unsure how to interpret the differences between these two sets of results.
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Related Issues (20)
- Conda package errors HOT 3
- Similarity score and plotting HOT 1
- Can't save changes to session HOT 2
- update 0.0.28 HOT 3
- the legend HOT 4
- How to visualize a gene on a large chromosome?
- Use clinker to visualize individual exons rather than whole gene?
- ValueError: not enough values to unpack (expected 2, got 1)
- Error in clinker HTML plotting function
- Errors in using gff and faa file
- The output result has no information HOT 4
- Locus inversion showing incorrect locations
- Possible bug in cluster similarity output (-mo option)
- -gf/--gene_functions not working?
- Problem with -gf and -cm parameteres HOT 3
- try example encouter error
- Gene and species limit HOT 1
- Broken pipe error when using clinker to plot gene clusters HOT 2
- Renaming coding sequence back to gene number HOT 2
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