Comments (1)
Dear Dearbhaile,
Very long branches usually indicate that there are many specific synteny clusters shared for the taxons on that branch. I think first use highly quality genomes, if some genomes are highly fragmented and poorly annotated, containing many TE related replicated proteins (can bring intra-genome blocks). This may affect synteny detection. So check the initial synteny blocks also helps, to see whether the blocks are all of high quality, if something weird exists.
from synnet-pipeline.
Related Issues (13)
- Wrong usage of shell scirpts parameter HOT 1
- tools for phylogenetic profiling HOT 2
- SynetBuilding- Diamond.sh HOT 1
- how to use the results performed by SynetBuild-X.sh? HOT 1
- MCScanX alternative HOT 1
- Segmentation fault HOT 1
- Minor fix suggestions for infomap.r and Phylogenomic_Profiling.r HOT 1
- Getting a size error when carrying out Phylogenetic profiling HOT 1
- there might be some species HOT 2
- SynetBuild-X.sh: line 132: detect_collinear_tandem_arrays: command not found HOT 1
- Species missing from the matrix HOT 1
- Error in check_gene_names(seq, annotation) , Sequence names in 'seq' do not match gene names in 'annotation' for: HOT 1
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from synnet-pipeline.